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Pay your employees: checks, paystubs, or direct deposit

Everything hangs off the run: paystub links, check printing on your own check stock, and the direct-deposit file for your bank.

1. Open the runIn Books & Payroll, click Employees, then the run's row on the Paychecks tab. Each employee line has a "paystub" link, an "email" link, and — if paid by check — "print check."
2. Print or save a paystubClick "paystub" to open the Earnings Statement in a new tab. Use your browser's Print (Ctrl/Cmd+P) and "Save as PDF," or send it to a printer. "email" sends it to the address on the employee.
3. Print a checkClick "print check" for one person, or "print checks" on the run's row for every paper check in the run, one after another. The page that opens has a Print button.
4. Line it up with your check stockOn the check page, pick your Check stock: a voucher check with the check on top, in the middle, or on the bottom, or three checks to a page. The first time, click "Print a test page" on plain paper, hold it against a blank check in front of a light, and use Move right and Move down until it lines up; then "Save these settings." In the print window use Scale 100%, Margins None, and headers and footers off.
5. Check numbers are automaticOn a paper check run, numbers are assigned in order as the run is approved — you never type them. Payroll numbers follow the highest check number already in that bank account's register.
6. They are in the bank register tooOpen Banking and pick the account the run was paid from: each check is a line there with its number, ready to match against the bank and to reconcile.
7. Start from your checkbook's numberPayroll counts on from the last check in the register. If your checkbook is at a different number, write your next check under Banking, "Write Check," with that number in the No. box, and payroll carries on after it.
8. Direct deposit: set up your bank onceOpen Chart of Accounts, click the Preferences chip, and find Payroll. Fill in Bank name, Bank routing number (9 digits) and Company ID from the bank (often your EIN). Your bank gives you both numbers when it sets you up to send payroll files; ask for ACH origination. Click Save. It says Run Payroll can pay by direct deposit now.
9. Direct deposit: employee bank detailsEach employee paid by direct deposit needs bank info saved in their "Sensitive data" section first. If anyone's missing it, the preview tells you exactly who and will not run until it is added or you switch to paper checks.
10. Download the NACHA fileRight after a direct-deposit run, the note at the top has a "Download the NACHA file" link. Later, the run's own row has a "bank file" link. Either one downloads the .ach file.
11. Send the file to your bankThe app builds the NACHA file; it doesn't transmit it. Upload the .ach file through your bank's business portal (or hand it off per their process) so they originate the deposits.