CheckMark Canadian Payroll: A Complete Guide for Small Businesses

Streamline Payroll with CheckMark Canadian Payroll: Step‑by‑Step SetupRunning payroll in Canada involves tax rules, deductions, and reporting deadlines that change with each province and line of business. CheckMark Canadian Payroll is designed to simplify that complexity by automating calculations, generating required remittances and tax forms, and keeping records organized for audits. This guide walks you through a step‑by‑step setup and shows best practices to get payroll running smoothly and accurately.

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Why choose CheckMark Canadian Payroll?

CheckMark has been tailored for Canadian payroll needs. It supports federal and provincial tax calculations, CPP/QPP, EI, taxable benefits, vacation pay, retroactive pay adjustments, and year‑end processing including T4s and summaries. Its strengths include localized tax rules, flexible pay schedules, and integration options with accounting systems.

Key benefits

• Accurate federal and provincial tax calculations
• Automated remittance and year‑end reporting
• Customizable pay schedules and deduction rules
• Recordkeeping suitable for audits

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Preparation: information and decisions before setup

Before you start entering data, gather these items and decide on payroll policies:

• Business number (BN) and payroll program account with the CRA
• Banking details for remittances and payroll deposits
• List of employees with SINs, addresses, start dates, birthdates (if needed for benefits), and classification (employee vs contractor)
• Pay schedules (weekly/biweekly/monthly), first pay date, and pay period rules
• Employment agreements specifying overtime, statutory holiday rules, vacation pay rate, and whether vacation is paid each pay or accrued
• Benefit plans and deduction amounts or formulas (RRSP contributions, group benefits, union dues, garnishments)
• Year‑end reporting preferences and responsible person for filing T4s/T4As

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Step 1 — Install and register CheckMark software

1. Download CheckMark Canadian Payroll from the official vendor site or install via your purchased media.
2. Run the installer and follow prompts; choose the Canadian edition where applicable.
3. Activate your license using the serial/key provided at purchase. Keep license and support contact info in a secure location.

Tip: If using a hosted/cloud version, create the administrator account and verify your email before proceeding.

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Step 2 — Configure company profile and tax settings

1. Open the Company (or Organization) setup screen. Enter legal business name, operating name, BN, payroll account number, address, and contact details.
2. Set default pay period (weekly/biweekly/monthly) and the company’s fiscal year end.
3. Verify federal defaults and choose province of operation (this determines provincial tax tables and CPP/QPP settings).
4. Enter banking details for payroll direct deposit and remittances; configure remittance frequency (monthly, quarterly, or by CRA schedule).
5. Enable electronic filing options (if supported) for CRA remittances and year‑end T4 uploads.

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Step 3 — Create employee records

1. From the Employees menu choose Add New Employee.
2. Enter full name, SIN, date of birth, address, start date, termination date (if applicable), and employment status.
3. Assign employee type (salaried/hourly), pay rate, and pay frequency.
4. Set tax information: TD1 federal and provincial amounts or exemptions. Enter CPP/QPP exceptions if applicable.
5. Configure deductions and contributions: union dues, RRSP, group benefits, garnishments, child support. For benefits, specify taxable vs non‑taxable amounts and company contributions.
6. For direct deposit, enter bank account and branch transit/Routing numbers. Validate deposits with a test run if desired.

Example fields to check:

• Salary/hourly rate, overtime multiplier, salaried annual amount
• Vacation pay percentage or accrual method
• Stat holiday pay calculation method (averaging vs regular rate)

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Step 4 — Set up payroll items and calculation rules

1. Define earnings codes (regular pay, overtime, bonus, vacation pay, commission). Assign default GL accounts if integrating with accounting software.
2. Configure statutory deductions: CPP/QPP rates, EI rate, federal and provincial tax tables. Ensure year‑to‑date tracking is enabled.
3. Create company contributions (employer CPP/QPP portion, employer EI portion, health tax employer contributions if applicable).
4. Establish benefit and deduction pools: set pre‑tax vs post‑tax treatment, caps (e.g., maximum pensionable earnings), and fixed vs percentage amounts.
5. If applicable, configure retroactive pay and lump‑sum calculation methods for adjustments.

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Step 5 — Enter opening balances and historical data

1. If migrating from another payroll system, import employee year‑to‑date (YTD) earnings and deductions to reflect accurate year‑to‑date totals. Most migrations allow CSV imports or direct conversions.
2. For each employee, enter YTD totals for gross pay, taxable benefits, tax withheld, CPP/QPP, EI, and other deductions.
3. Verify totals against prior pay stubs or last payroll remittance to CRA to avoid discrepancies at year‑end.

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Step 6 — Run the first payroll (test run)

1. Create a pay run for the selected pay period. Add employees and confirm hours/salary amounts.
2. Review calculated gross pay, statutory deductions, employer contributions, net pay, and remittance totals.
3. Use the preview or report feature to inspect deduction breakdowns, GL posting summary, and bank deposit file (for direct deposit).
4. If errors are found, adjust employee records or payroll item settings and re-run.
5. Once confirmed, finalize the pay run to generate pay statements and remittance reports.

Checklist before finalizing:

• Correct employee tax exemptions and TD1 entries
• Proper overtime and vacation calculations
• Accurate pensionable/insurable earnings caps applied

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Step 7 — Remittances and electronic filing

1. Generate remittance summaries and CRA-compatible reports (PD7A summary for payroll remittances).
2. Use the software’s electronic filing/electronic funds transfer (EFT) features if available to submit payments and remittances to the CRA and provincial authorities. Otherwise, use CRA My Payment or your banking portal with the remittance account and amounts provided.
3. Keep copies of remittance receipts and confirmations stored with payroll records.

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Step 8 — Month‑end and year‑end procedures

Monthly/quarterly:

• Review payroll journal entries and reconcile with accounting software.
• Reconcile bank payroll account and direct deposit totals.
• Check CRA remittance history and ensure no outstanding liabilities.

Year‑end (T4/T4A):

1. Ensure all YTD figures are correct and any late adjustments have been applied.
2. Generate T4 slips and T4 Summary for employees. Verify SINs and addresses to avoid rejections.
3. File T4s electronically via the CRA’s Webfiling (or through CheckMark’s electronic filing if provided) and distribute employee copies.
4. Prepare ROE (Record of Employment) submissions for layoffs or terminations as required.

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Tips and best practices

• Maintain a payroll calendar with pay dates, remittance due dates, and year‑end deadlines.
• Run a small parallel test for one pay period when changing systems to catch configuration errors.
• Keep backup copies of payroll data before major updates or migrations.
• Document payroll policies and maintain a secure file of employee TD1 forms and authorizations.
• Regularly update CheckMark software to receive tax table updates and security patches.

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Troubleshooting common issues

• Wrong tax calculations: recheck employee TD1 entries, province selection, and payroll tax table version.
• Incorrect CPP/EI: ensure correct pensionable/insurable marked earnings and YTD opening balances.
• Direct deposit failures: validate bank routing numbers and ensure file format meets bank specifications.
• Year‑end mismatches: reconcile YTD totals against prior system exports and CRA account statements.

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Integrations and scaling

CheckMark supports integration with accounting packages (export/import of GL entries), time‑tracking systems, and direct deposit processors. For growing businesses:

• Use automated imports for timecards to reduce manual entry.
• Segment payroll by business unit or location for clearer reporting.
• Consider outsourced payroll services for high headcount or multi‑province operations.

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Final checklist before going live

• Company profile, BN, and payroll account verified.
• All active employees added with correct SINs, TD1s, and banking info.
• Earnings, deductions, and employer contributions configured.
• Year‑to‑date balances imported and reconciled.
• Successful test pay run completed and remittance workflow validated.

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Streamlining payroll with CheckMark Canadian Payroll requires careful setup but pays off through accurate statutory compliance, reduced manual work, and clearer reporting. Follow these steps, keep records organized, and update settings as regulations change to keep payroll running smoothly.