Can I run this employee through payroll and then let him write a check manually for the payment?

Hello there, @beyor46.

Yes, taxes are added to an employee's auto payroll payment when writing a manual check in QuickBooks Online Payroll (QBOP). Let me share further details about this and guide you on how.

When you're using QBOP, your employees' taxes will automatically be added or calculated every time you run payroll (via Payroll menu). However, there'll be no taxes calculated in case you're manually writing a check via the + New button.

On the other hand, based on your description, you may be set up and schedule your payroll to run automatically (Auto Payroll) with QBOP. If your employee is enrolled in Auto Payroll and you need to pay them outside your normal payroll schedule, you can pause it for a pay period. Then, it'll start again on your next pay run. To do this, here's how:

1. Go to Payroll, then Run Payroll.
2. Select Prefer to pay manually this period? on the employees, you wish to pay manually.
3. Enter the date, pay schedule, and edit any pay items for this payroll.
4. Select Preview payroll and then Submit payroll.

If you wish to stop paying some employees or create paychecks manually via Auto Payroll, you need to unenroll them (temporarily). Please make sure to sign in to QuickBooks as the primary admin to do these steps:

1. Select Settings ⚙ or Gear icon, then Payroll Settings
2. In the Auto Payroll box, select Edit ✎.
3. Select the Select employees for Auto Payroll option.
4. Select one or more of the enrolled employees.
5. Select Save Changes.
6. Review the confirmation window, then select Done.

You can read this article to learn more about managing Auto Payroll in QBOP: Make temporary or permanent changes to your Auto Payroll in QuickBooks Online Payroll.

Also, there are a variety of payroll reports you can use to view information about your business finances and employees in QBOP. You may want to check out this article to see the complete list and guide you about accessing and customizing the report you need: Run payroll reports in QuickBooks Online Payroll.

Let me know if you have other payroll concerns or questions about managing employees in QBOP. I'm always ready to help. Take care, @beyor46.