Can I pay an employee a seperate paycheck. He's on auto payroll and I missed a week

It's great that you're looking for a way to correct the missed pay without disrupting your regular automated process, Garry.

The good news is that QuickBooks Online Payroll is designed to handle this exact situation using an Unscheduled Payroll, also known as a one-time pay run. This process allows you to pay a single employee for a specific, missed pay period without affecting your employee's regular Auto Payroll schedule.

Here’s how you can process a one-time payroll check:

1. Navigate to the Payroll tab under the My apps menu, and then select Employees.                   
2. In the upper right corner, click the Run Payroll. If prompted, select the same pay schedule the employee is on.
3. On the payroll review screen, deselect all employees except the one you missed.
4. Verify and adjust the Pay period and Pay date.                         
5. For the selected employee, verify that the hours and salary for the missed week are correct. If necessary, select the Action or three-dot icon and click Edit paycheck to manually enter the correct earnings for that single missed week.                          
6. Click Preview Payroll to check the net pay and taxes, and then Submit payroll.

After you submit this unscheduled payroll, your employee's next regular Auto Payroll run will proceed as scheduled, completely unaffected by this correction.

Your careful attention to correcting this will keep your employee's year-to-date wages accurate and prevent any disruption to your regular payroll routine. Don’t hesitate to reach out if you have any other questions or concerns.