Help Center

Running payroll

Payrollix calculates wages, taxes, and deductions automatically. You review and approve.

8 articles

Run a regular payroll

Start, preview, approve, and process a scheduled payroll run from the dashboard.

Off-cycle, bonus & correction payrolls

Pay outside the regular schedule: bonus, termination, correction, or fully off-cycle runs.

Auto-pilot payroll

Turn on auto-run so Payrollix creates, approves, and processes each payroll on schedule — and skip or override when you need to.

Mid-year YTD setup

Enter prior-provider year-to-date wages, taxes, earnings, and deductions per quarter or per check date — the complete step-by-step, including how to set up earnings/deduction types first so they appear as their own columns, and how to fill the grid in Excel via CSV.

Payroll history & edits

Browse past payrolls, drill into a run, edit a draft, recalculate, and see the same data in each portal.

Print paychecks: the check designer, stock, and alignment

Use the Check Printing designer to match any check stock: pick a template, set paper size, check position and height, fine-tune each element, and watch a live preview (with a ruler). Then download checks — or let CheckFlo print and mail them.

S-Corp >2% shareholder health insurance & HSA

How to set up, tax, and report health insurance premiums and HSA contributions for a >2% S-corporation shareholder — activation in Client Settings, the per-employee flag, and the SH Ins/SH HSA columns on Run Payroll.

Set your payroll check numbers

Set the starting check number so printed payroll checks match your check stock, skip ahead when needed, and understand the paper-check vs. manual/cash payment methods.