SOP: Payroll Step 6

Learn how to process payroll efficiently, including handling commissions, adjusting deductions, and managing PTO payouts. This guide walks you through common payroll scenarios, troubleshooting, and best practices for accurate payroll management.

March 30, 2026 By Jessica Esslinger

In this guide, we'll learn how to review and process payroll, including handling commissions, adjusting deductions, and troubleshooting common issues that may arise during payroll calculation. We will also cover how to verify pay details for each employee and ensure all changes are accurately reflected before final approval.

This process helps maintain accurate payroll records and ensures employees are paid correctly for each pay period.

Let's get started

Okay. We left off with Eric handling his commissions differently so he can have them directly deposited into his preferred account. The reason we used the process to add, adjust, or estimate pay separately is because this functions as a "manual check," and it will...

We need to ensure the pay date and week match the current pay date and week being entered. If you see an error message, you likely already clicked "Calculate Pay" on your payroll. If you're following along with me, you should be fine. We want to make sure it's the same week number. The pay date is the 27th, so it is included in that payroll.

Now, we will go back to proc. If you want to review it, you can use print pay statement for a quick look at what it shows.

Step #3: Click on "Process ▼" — Click on "Process ▼"

Step #6: Click on "Print pay statement" — Click on "Print pay statement"

Here is the commission. Here are his deductions, 401, and the amount that will be deposited into his checking account. Okay.

Step #7: Click on "← Back" — Click on "← Back"

You can save that if you want, but it's not required.

I will process the payroll dashboard.

Step #11: Click on "Process" — Click on "Process"

Step #12: Click on "Payroll Dashboard" — Click on "Payroll Dashboard"

We will go back to Resicon. We will go to Commissions.

Step #13: Click on "Manage payroll" — Click on "Manage payroll"

Oh, just kidding. If you go under Other Payments, you can see this is the additional payment we made to Eric.

Step #14: Click on "Other Payments" — Click on "Other Payments"

Step #15: Click on "Additional Payments" — Click on "Additional Payments"

That will appear in the pay run when we review our checks and balances.

That one looks good. I think that might be it for everyone.

Step #19: Click on "← Back to Payroll Dashboard" — Click on "← Back to Payroll Dashboard"

The only one I need to go back and update is Health Alliance. I have to add a code for the advance because it needs to be entered differently. And I'll probably do a separate... I think I will do a separate one. Video on each of the templates. Once that looks good, we can start calculating payroll for each of these.

I like to review each item one by one and check the master work paper of our notes to ensure everything highlighted for that check date looks correct.

Step #24: Drag "03/27/26" — Drag "03/27/26"

Step #25: Drag "03/27/26" — Drag "03/27/26"

Step #26: Drag "Telly Miller on LOA as of 3/17/26" — Drag "Telly Miller on LOA as of 3/17/26"

Let's start with that.

We will start with Comp 1 as an example. This will serve as a guide for the remaining codes.

Step #28: Click on "( NR2 - TXU )" — Click on "( NR2 - TXU )"

Step #29: Double-click on "FJV )" — Double-click on "FJV )"

Step #30: Click on "CompOne ( U4F )" — Click on "CompOne ( U4F )"

Comp 1, calculate payroll.

Step #32: Click on "Calculate payroll" — Click on "Calculate payroll"

Once it appears, it will say "awaiting approval." Never hit approve until it is a Wednesday afternoon around 1:00 or 2:00 PM. Only approve after you have reviewed all necessary work papers to ensure everything looks correct.

Step #33: Click on "View details" — Click on "View details"

I like to review paycheck totals.

Step #34: Click on "Register" — Click on "Register"

This is my main one and the statistical summary as well. The first one I will look at is the payroll register. I will download it.

Step #35: Click on "Download selected" — Click on "Download selected"

I will click that to open it and review.

Step #36: Click on "RegisterCheckLeve" — Click on "RegisterCheckLeve"

We have a few things to review. The first one is Autumn Moore.

Step #37: Double-click here — Double-click here

Step #38: Click on "03/27/26" — Click on "03/27/26"

Step #39: Click on "Autumn Moore" — Click on "Autumn Moore"

We need to ensure she has nothing in this paycheck.

Step #40: Click on "Jess already processed final payment on 3/13/26" — Click on "Jess already processed final payment on 3/13/26"

I like to quickly use Control + F to check if "Autumn" is present.

Step #42: Click on "Enable Editing" — Click on "Enable Editing"

Type "Ctrl + F"

She is not.

Type "autu"

Step #47: Click on "Find Next" — Click on "Find Next"

Okay?

If you want to double-check, scroll down and look for her name in the Ms, but it is not there. Okay. We will go here and click "Complete."

Type "c"

Next is Julia and her pay increase.

Type "c"

Step #56: Click on "will be eligible for implementation bonuses in the future" — Click on "will be eligible for implementation bonuses in the future"

Type "c"

Step #58: Drag "Dru Hamilton" — Drag "Dru Hamilton"

Step #60: Click on "this check should be $ 2961.54" — Click on "this check should be $ 2961.54"

We need to ensure it is 2961.54.

Step #62: Click on "INP - PTO - Paid Time Off 75.99" — Click on "INP - PTO - Paid Time Off 75.99"

Type "Ctrl + F"

So, Julia, 2961.54.

Type "jul"

Step #66: Click on "Find Next" — Click on "Find Next"

Step #67: Click on "Find Next" — Click on "Find Next"

That looks good. We will mark it as complete.

Step #70: Double-click here — Double-click here

Drew Hamilton, ensure there are only 40 hours of PTO and that all these deductions are included.

Type " co + Tab"

Step #74: Double-click here — Double-click here

Type "Com + Tab"

Step #76: Drag ". So for this pay only pay 40 hours of PTO" — Drag ". So for this pay only pay 40 hours of PTO"

Step #77: Click on "So for this pay only pay 40 hours of PTO" — Click on "So for this pay only pay 40 hours of PTO"

Drew, you have 40 hours of PTO.

Type "dru"

Step #81: Click on "Find Next" — Click on "Find Next"

Step #82: Double-click here — Double-click here

Step #83: Click on "Find Next" — Click on "Find Next"

He has no deductions.

We need to go back and add a worksheet to adjust his deduction. I'll note that. Next is Telly Miller, who is only paid for the hours listed on the time card.

Step #87: Double-click here — Double-click here

Step #89: Click on "Only pay for hours on timecard ( should be 48.42 hours )" — Click on "Only pay for hours on timecard ( should be 48.42 hours )"

Should only be 48.42. We will look up Telly Miller.

That was what appeared on her time card.

Step #93: Click on "Find what" — Click on "Find what"

Type "telly"

Step #95: Double-click on "Find Next" — Double-click on "Find Next"

Everything looks good.

Step #98: Click on "ACC Accident Ins" — Click on "ACC Accident Ins"

Okay. It didn't mention deductions.

If you're unsure, ask.

Okay, complete.

Kaitlin Bradley, ensure her pay is 2000.

104

Type "c"

Step #106: Click on "effective" — Click on "effective"

Her salary is 2000.

109

Type "Ctrl + A"

110

Type "radl"

Step #111: Click on "Find Next" — Click on "Find Next"

Mark it complete.

And Linda Roberts, severance pay...And Roberts'...

116

Type "comp"

Step #118: Click on "Pay separation compensation $ 1,225.70" — Click on "Pay separation compensation $ 1,225.70"

Step #119: Click on "Pay increase effective" — Click on "Pay increase effective"

122

Type "rober"

Step #123: Click on "Find Next" — Click on "Find Next"

Step #124: Click on "Find Next" — Click on "Find Next"

Step #125: Click on "Find Next" — Click on "Find Next"

Step #126: Click on "Find All" — Click on "Find All"

Severance pay looks great.

128

Type "ts"

Step #129: Click on "Find Next" — Click on "Find Next"

Okay.

That's a great example.

Step #134: Click on "Complete" — Click on "Complete"

135

Type "c"

We will make this change and retrieve their deductions.

Step #138: Click on "Only pay for hours on timecard" — Click on "Only pay for hours on timecard"

I will exit, make changes.

Step #144: Click on "Make changes" — Click on "Make changes"

I will go to Drew's last paycheck.

With profile, pay, and pay profile.

146

Type "dru"

Step #147: Click on "People ▼" — Click on "People ▼"

Step #148: Click on "Dru Hamilton с" — Click on "Dru Hamilton с"

150

Click on "Pay Profile"

Here are the deductions. You can take a quick screenshot, or you can copy and paste.

Step #151: Click on "Deductions >" — Click on "Deductions >"

Step #154: Drag "24.52 Other ( Managed by Benefits )" — Drag "24.52 Other ( Managed by Benefits )"

So then I'm going to...

155

Type "Ctrl + C"

156

Type "Ctrl + C"

Let's see if that works.

Step #159: Right-click on "Insert Row" — Right-click on "Insert Row"

Paste special.

Step #160: Click on "FSA - Flexible Spendi" — Click on "FSA - Flexible Spendi"

That worked better.

161

Type "Esc"

I'll remove that.

Step #163: Click on "Other ( Managed by Be" — Click on "Other ( Managed by Be"

Okay.

Step #165: Click on "Other" — Click on "Other"

We need to keep these deductions and add those in.

Okay.

Step #170: Click on "$ % 950000" — Click on "$ % 950000"

Step #172: Double-click here — Double-click here

I need to go back.

Process payroll dashboard. Manage payroll. Add worksheet.

Step #176: Click on "< BACK" — Click on "< BACK"

Step #177: Click on "Process ▾" — Click on "Process ▾"

Step #178: Click on "Payroll Dashboard" — Click on "Payroll Dashboard"

Step #179: Click on "Manage payroll" — Click on "Manage payroll"

Step #180: Click on "Add worksheet" — Click on "Add worksheet"

We will choose "Adjust Deductions."

Step #181: Click on "Select one ..." — Click on "Select one ..."

Step #182: Click on "Deduction - Adjust" — Click on "Deduction - Adjust"

Next.

184

Type "Deduction - Adjust"

Step #186: Click on "Next >" — Click on "Next >"

We will choose Drew.

Step #187: Click on "Search by name or positic" — Click on "Search by name or positic"

Okay.

188

Type "dru"

I'm going to do a... ""

Oopsies.

Step #194: Double-click here — Double-click here

I meant to move to the side instead of zooming in.

Okay.

Step #196: Double-click here — Double-click here

Step #197: Double-click here — Double-click here

Step #198: Double-click here — Double-click here

Step #200: Drag "93 STD - STD Post Tax" — Drag "93 STD - STD Post Tax"

This will be a positive because we need to deduct it from the paycheck. Then, I will enter the information.

The first three letters are the code, which is helpful because you don't have to scroll through it. "" New Life Medical, Roth, STD, and vision. Okay.

202

Type "acc + Tab7.63 + Tabcre + Tab5.19 + Tabden + Tab9.94 + Tabfsa + Tab57.69 + Tablic + Tab1.12 + Tablif + Tab7.28 + Tabmed + Tab24.52 + Tabrth + Tab25 + Tabstd + Tab27.66 + Tabvis + Tab2.05"

Next, double-check the numbers to ensure everything looks correct. Click auto-balance, then done.

Step #204: Click on "AUTO BALANCE" — Click on "AUTO BALANCE"

Step #205: Click on "DONE" — Click on "DONE"

That is the only one left to double-check, so I will click calculate payroll.

Step #207: Click on "Calculate" — Click on "Calculate"

I will go to the same payroll register, download the selected file, and open it.

Step #209: Click on "Register - Pay Check Level Totals" — Click on "Register - Pay Check Level Totals"

Step #210: Click on "Verification Report" — Click on "Verification Report"

Step #211: Click on "RegisterCheckLeve" — Click on "RegisterCheckLeve"

Control-F, Drew.

Step #212: Double-click on "Earnings 4" — Double-click on "Earnings 4"

213

Type "Ctrl + F"

Still not showing up.

214

Type "dru"

Step #215: Click on "Find Next" — Click on "Find Next"

Huh. Let's begin troubleshooting.

Step #217: Click on "Enable Editing" — Click on "Enable Editing"

We are going to make changes.

Step #219: Click on "Unused Deduction" — Click on "Unused Deduction"

Step #220: Click on "Make changes" — Click on "Make changes"

Hmm. We might need to select "replace" instead of "adjust."

Step #221: Click on "Manage payroll" — Click on "Manage payroll"

Step #222: Click on "Wrksh003" — Click on "Wrksh003"

I will do a replacement one.

Step #223: Click on "DONE" — Click on "DONE"

I will delete this one and add worksheet replace.

Step #226: Double-click on "OK" — Double-click on "OK"

Step #227: Click on "+ Add worksheet + Add time / time off worksheet" — Click on "+ Add worksheet + Add time / time off worksheet"

I will go through the same exercise to see if it appears quickly.

Step #229: Click on "Deduction - Replace" — Click on "Deduction - Replace"

Step #230: Click on "Next >" — Click on "Next >"

Step #231: Double-click on "< all employees >" — Double-click on "< all employees >"

Step #232: Click on "Search by name or posi ..." — Click on "Search by name or posi ..."

233

Type "fru"

235

Type "dru"

Step #237: Click on "Submit" — Click on "Submit"

Okay. I completed the replace deduction worksheet instead. I have them here. I will auto-balance, press done, and then calculate the payroll again to see if it appears. It's still not there.

Since I have tried everything I can think of, we may have to see... Take Drew off leave. I will discuss this with Erica. In this case, we need to take him off leave to process the deductions. There should be a toggle or similar option for this. Um... Oh!

I know the problem. Just kidding. We recorded 40 hours of PTO, but since we didn't select a rate, it isn't being calculated or included. Okay. That's what it is.

We will make changes. I made a mistake. Sometimes, if you make too many changes, it says we need to give it a second. We will wait for a few minutes. I will pause now and resume after a short wait. Okay.

Drew's deductions aren't showing up because I only entered 40 hours of PTO but did not enter a rate. Generally, this person is salaried.

Step #238: Click on "AUTO BALANCE" — Click on "AUTO BALANCE"

Step #239: Click on "DONE" — Click on "DONE"

Step #240: Click on "Last calculated at 12:22 PM on 03/24/2026" — Click on "Last calculated at 12:22 PM on 03/24/2026"

Step #242: Drag "PT0001" — Drag "PT0001"

That was my mistake, but it's a good learning experience. Manage payroll. We will cover PTO and time off.

Step #243: Click on "Payroll" — Click on "Payroll"

Step #244: Click on "Download selected" — Click on "Download selected"

We have hours.

Step #245: Click on "194 KB • Done" — Click on "194 KB • Done"

Oh wait, that was the wrong one.

Let's check its status. Maybe I didn't add his PTO.

Step #248: Click on "Find Next" — Click on "Find Next"

That's why—because he used PTO, I have to calculate it manually. Because his PTO is in the batch ready, it is deducted from his salary. However, since he is on a leave of absence, he is not receiving a salary.