How to Run Payroll End to End
The complete walkthrough of a payroll cycle in Pixelbase — from collecting hours to filing 941s and delivering pay stubs.
Three clicks to run payroll.
In Pixelbase you review the auto-populated payroll preview, approve, and we handle the rest — direct deposits, tax remittance, federal + state filings, year-end W-2s. The walkthrough below is the long version.
Run Payroll NowThe payroll cycle, step by step
Collect hours and time-off
For hourly employees: hours worked, overtime, breaks. For salaried: confirm no unpaid leave. Pixelbase imports from time tracking or accepts manual entry.
Review gross-to-net preview
See each employee's gross pay, federal/state withholdings, FICA, 401(k)/HSA deductions, garnishments, and final net. Catch errors before approving.
Approve the run
Lock in the numbers. Once approved, the system schedules direct deposits, batches tax remittances, and queues filings.
Direct deposits hit accounts
Standard ACH: 1–3 business days. Same-day ACH: same business day if approved before 1pm ET. Pay stubs delivered electronically.
Tax payments remit automatically
Federal: EFTPS. State: each state's portal. Deposits on the schedule the IRS assigned you (semiweekly or monthly).
Filings queued
941 each quarter, 940 annually, state unemployment + withholding quarterlies, W-2s + W-3 by January 31. All automatic.
Pick a pay schedule
Some states regulate the minimum cadence (CA requires at least semimonthly for most employees). Pick the one your team prefers within state rules.
Hourly workers, construction, restaurants
Most common — most W-2 employees
Salaried teams, simpler accounting
Senior salaried staff, owner-only S-Corps
What Pixelbase automates vs DIY
Mistakes that derail a payroll run
Things to check before approving
- Missing hours. If an hourly employee has zero hours, double-check whether they actually worked.
- Forgotten overtime. Anything over 40 hrs/week (federal) or daily limits in CA must be at 1.5×.
- Wrong pay rate. Raises and rate changes need to be entered before the run, not after.
- Stale W-4.If an employee updated their W-4 and you didn't enter it, their withholding will be off.
- Insufficient bank balance. Make sure your operating account can cover net pay + employer taxes before approving.
Edge cases worth knowing
Off-cycle bonuses
Bonuses can run as supplemental wages (flat 22% federal withholding up to $1M) or aggregated with the next regular paycheck.
Wage garnishments
Court-ordered withholdings (child support, IRS levies, student loans). Take priority over regular deductions. Pixelbase handles automatically.
Final paychecks
Many states require same-day or next-day payment of all wages owed on termination. CA: same day for involuntary, 72 hr for voluntary.
Multi-state employees
Remote workers in different states trigger payroll tax registration in each state. Some states have reciprocity agreements.
Common misconceptions
"I run payroll once a month so I'll do it later."
Payroll deadlines drive tax remittance + filing deadlines. Run early and approve early — the IRS doesn't care that you got busy.
"Contractors can be paid through payroll."
Contractors get 1099-NECs and are paid via accounts payable, not payroll. Mixing them up causes misclassification audits.
"Pre-tax 401(k) deductions reduce my employer taxes."
They reduce employee income tax + employer FICA on the deducted amount. Both win.
Run payroll, end to end.
Pixelbase Payroll handles every step automatically. You approve. We pay your team, pay the government, file the forms, and deliver pay stubs. No spreadsheets, no deadline panic.