Mid-year YTD setup

Last updated 2026-09-28For: Accountant, Small business

This guide covers: When YTD setup is required, Setting up earnings & deductions first, Picking the takeover type, The entry grid and every column, Entering earnings, Entering taxes, Entering deductions (pre-tax, post-tax, general/per-plan, garnishments), Reimbursements & wage bases, Per-quarter and per-check entry, and Save/supersede.

When YTD setup is required

What it does: YTD setup captures the wages and taxes a previous provider already paid in the current tax year — so Payrollix's first run picks up at the right Social Security cap, Additional Medicare threshold, SUTA taxable wage cap, and FUTA wage base, and so W-2s/941s/state returns are complete. Without it, the engine treats the first Payrollix run as the employee's first paycheck of the year.

Where: Client sidebar → Payroll → YTD Setup (/clients/{clientId}/ytd-setup).

Steps: You need YTD setup when:

  1. The client is a mid-year takeover from another provider in the current tax year.
  2. The client paid the employee outside Payrollix before going live (manual checks, a prior payroll system).
  3. You're correcting or backfilling historical data.

Who: Accountant or SMB admin.

Notes: The bulk importer does not capture YTD — use this page. After saving, every new payroll run reads against the per-period YTD ledger when computing wage caps, withholding thresholds, and W-2 boxes.

Before you start — set up the client's earnings & deductions

What it does: Defines the pay types and deduction types the client used with their prior provider so their year-to-date amounts land classified (by name) on paystubs, reports, and W-2s — instead of as a generic lump. This is the single most important prep step.

Where: Client sidebar → Compensation → General Deductions (and the client's benefit/deduction and earning settings).

Steps:

  1. General deductions (union dues, charity, uniforms, "Shirt", equipment, loans/advances, etc.): create a plan for each one under General Deductions before opening YTD Setup. Give each a clear code and name (e.g. code SHIRT, name "Shirt"). Every active plan then appears as its own column in the YTD grid, so you type the year-to-date amount straight into the "Shirt" or "Child Care" column and it's stored against that plan.
  2. Pre-tax benefits (§125 health/HSA/FSA, 401(k)/403(b), etc.) and post-tax deductions (Roth, other): these roll up into the single Pretax Ded and Posttax Ded columns (a per-quarter total each) — you don't need a separate plan per benefit for YTD, just the quarter totals.
  3. Standard earning types (Regular, Overtime, Holiday, PTO, Sick, Bonus, Commission, Tips) are already built-in columns — no setup needed; turn on Show all fields to itemize them (see below).

Who: Accountant or SMB admin.

Notes: If you skip step 1 and enter a general deduction into the generic "General Ded" column, it still totals correctly but shows as a generic "Deduction" line rather than by name. Defining the plan first (or re-entering through the per-plan column) is what makes it read as "Shirt." See Deductions & earnings and Pre-tax vs post-tax deductions.

Who appears in the grid (add employees first)

What it does: The grid seeds one row per employee under each period. If the client has no employees yet, you'll see only the column headers and nothing to type into — add the roster first.

Where: Client sidebar → Employees (/clients/{clientId}/employees).

Steps:

  1. Make sure the client's workers exist as W-2 employees before opening YTD Setup. The page shows an amber banner (with an Add Employees link) whenever there are no rows to enter against.
  2. The grid includes:
    • Active W-2 employees.
    • Terminated W-2 employees who had wages in the tax year — someone let go mid-year (say in Q2) still needs their Q1/Q2 wages on their W-2 and the 941, so they appear with a "terminated" tag. Only people terminated before the tax year began are left out.
  3. 1099 contractors are excluded — they don't get W-2 wage/tax YTD, so they're not shown.

Who: Accountant or SMB admin.

Notes: To surface a terminated employee who isn't showing, confirm their record is a W-2 worker and that their termination date falls within (or after) the selected Tax Year. See Add an employee and Terminate an employee.

Pick the takeover type

What it does: Sets the granularity of entry — a lump per closed quarter, or one row per check date.

Where: The Tax Year picker + Takeover type card at the top of the page.

Steps:

  1. Pick the Tax Year.
  2. Pick the takeover type:
    • Closed-quarter takeover (closed_quarters) — the prior provider already filed each closed quarter's 941. Enter one lump row per closed quarter per employee. Feeds annual W-2/W-3/940 and supports 941-X amendments; excluded from any Payrollix 941 for those quarters.
    • Mid-quarter takeover (current_quarter) — the prior provider paid inside the current open quarter and Payrollix will file this quarter's 941. Enter one row per check date. Required so Schedule B (semi-weekly depositors), state quarterly wage detail, and the IRS next-day-deposit threshold are accurate.
    • Prior-quarter per-check (prior_quarter_checks) — same per-check detail but for check dates in an already-closed quarter. Use when you want full per-paycheck history in Payrollix (for payroll reports / workers'-comp audits / QuickBooks reconciliation) rather than one lump; like closed quarters, it's kept out of that quarter's Payrollix 941.

Who: Accountant or SMB admin.

Notes: One save can mix modes across quarters. The page auto-detects the type from existing saved data when you reopen it.

The entry grid — every column, and "Show all fields"

What it does: Each employee is a row; each money field is a column, grouped by type. Common fields show by default; Show all fields reveals the advanced columns.

Where: The grid for each period. Toggle Show all fields (top of the grid) to expand.

Columns by group:

  • Earnings — Gross (always shown; the authoritative total). Under Show all fields: Regular, OT, Holiday, PTO, Sick, Bonus, Commission, plus tips detail (Tips, Tips (Card), Tips (8% Alloc)), Service Chg, and S-Corp shareholder Health/HSA.
  • Employee taxes — Federal, State, Local, School Dist, SS (EE), Medicare (EE), Add'l Medicare, SDI/PFML (EE). Advanced: Local (Res), LST/OPT (EE). State-gated: VT CCC (EE).
  • Employer taxes — SS (ER), Medicare (ER), FUTA, SUTA. Advanced: SDI/PFML (ER), 401(k) Match (ER), employer contributions, Workers' Comp (ER). State-gated: CA ETT, VT CCC (ER), CO OPT, OR Transit.
  • Deductions — Pretax Ded, Posttax Ded, Garnishments, plus one column per active general-deduction plan (e.g. Shirt, Child Care). The generic General Ded catch-all is under Show all fields.
  • Reimbursements — Reimb (non-tax).
  • Wage bases (advanced) — SS Wages, Medicare Wages, Add'l Medi Wages, FUTA Wages, WC Wages, Fed Box 1 Wages, State Wages, SUTA Wages.

Who: Accountant or SMB admin.

Notes: State-gated columns only appear for clients in that state. The Totals across all periods card updates live as you type.

Entering earnings

What it does: Records gross pay and, optionally, its breakdown by type.

Steps:

  1. Enter Gross for each employee/period — this is required and drives net-pay math.
  2. If you want the breakdown on reports and W-2s, turn on Show all fields and split gross across Regular / OT / Holiday / PTO / Sick / Bonus / Commission / Tips. The itemized amounts should sum to Gross.
  3. If you leave the breakdown blank, the whole Gross is treated as Regular pay (the classic single-Gross behavior).

Who: Accountant or SMB admin.

Notes: Enter Tips where applicable so W-2 Box 7/8 and Form 8027 are correct. Imputed/non-cash and S-Corp shareholder health are informational tags already inside taxable wages — enter them only if your source figures break them out.

Entering taxes

What it does: Records the employee-withheld and employer taxes the prior provider already paid.

Steps:

  1. From the prior provider's 941, enter Federal, SS (EE), Medicare (EE), SS (ER), Medicare (ER), and FUTA.
  2. From the client's state quarterly returns, enter State, Local/School Dist (where applicable), and SUTA.
  3. Add Add'l Medicare for high earners, SDI/PFML for states that have it, and any state-gated columns that appear (CA ETT, OR Transit, etc.).

Who: Accountant or SMB admin.

Notes: Leave a column at 0 when it doesn't apply. Payrollix reconstructs the taxable wage bases (FUTA/SS/Medicare) from the taxes you enter, so you usually don't need the Wage-bases columns at all (see below).

Entering deductions

What it does: Records year-to-date deductions, classified so they render correctly.

Steps:

  1. General deductions — for each plan you defined (Shirt, Child Care, union dues, uniforms, loan repayments, etc.), type the YTD amount into that plan's column. It's stored against the plan's code and shows by name on stubs/reports.
  2. Pre-tax deductions — enter the quarter's total §125/401(k)/HSA/FSA in Pretax Ded (one number). These reduce taxable wages.
  3. Post-tax deductions — enter the quarter's total (Roth, other post-tax) in Posttax Ded.
  4. Garnishments — enter the YTD garnishment total in Garnishments.

Who: Accountant or SMB admin.

Notes: The generic General Ded column (under Show all fields) is a catch-all for a general deduction that has no plan — it totals correctly but shows as a generic "Deduction." Prefer the per-plan columns so the amount is labeled. All deduction columns reduce net pay; pre-tax additionally reduces the taxable-wage bases.

Reimbursements & wage bases (advanced)

What it does: Reimbursements add non-taxable money to net; wage-base columns let you override the taxable bases when a cap or pre-tax exclusion makes them differ from gross.

Steps:

  1. Reimbursements: enter any non-taxable (accountable-plan) reimbursement in Reimb (non-tax) — it's added to net and shows on the paystub like a live-run reimbursement.
  2. Wage bases: leave these blank in almost all cases. Payrollix defaults them to gross and reconstructs FUTA/SS/Medicare taxable bases from the taxes you entered. Only fill a wage-base column when the true taxable base differs from gross (a mid-year SS-cap crossover, a heavy pre-tax employee, a state base cap) and you know the exact figure from the prior provider.

Who: Accountant or SMB admin.

Notes: Fed Box 1 Wages and State Wages default to gross when blank because the 941/W-2 forms sum them — don't zero them out by accident.

Save & supersede

What it does: Persists the YTD rows; later edits supersede prior rows rather than overwriting (originals stay in the DB for audit).

Where: Bottom of the page — Save YTD Data, and Mark superseded (red) to clear a year.

Steps:

  1. Click Save YTD Data. One ytd_setup row is written per (employee, period), marked completed.
  2. To correct, edit the grid and Save YTD Data again — the prior rows for the employees you re-submitted are marked superseded and the new ones become active.
  3. To clear the whole year, click Mark superseded and confirm. Nothing is hard-deleted.
  4. Start the first real run from the green Next Steps footer → Create New Payroll.

Who: Accountant or SMB admin.

Notes: Re-saving is scoped to the employees in the submission — an employee you don't include is left untouched (this protects terminated staff's prior-quarter wages). So when you re-open to fix one person, that's fine; but if you want a clean full re-entry, include everyone. Reports, 941, W-2, and paystubs all read only the current (non-superseded) rows.

Related: Deductions & earnings · Pre-tax vs post-tax deductions · Garnishments · Run a regular payroll · How Payrollix files your taxes.

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