Hello, @WEST2024. It's great to see you focusing on clarity in your payroll process. You can manage vacation payouts separately in QuickBooks Online (QBO), and I’m here to help.
To issue a vacation payout for your employee via a separate check, you'll need to run payroll twice for the same pay period. The first run should exclude the vacation pay, while the second run will be just the vacation pay.
Here's how to do it:
1. Navigate to the Payroll menu and open the Employees tab.
2. Select Run payroll.
3. Choose a pay schedule and click Continue.
4. Make sure the Pay period and Pay date are accurate.
5. Check the box next to your employee's name.
6. Fill in the required columns, leaving the Vacation pay column blank.
7. When you're ready, hit Preview payroll and then Submit payroll.

8. For the second paycheck, repeat steps 1 through 4.
9. Click the Create another check button and tick the box next to your employee's name.

10. Enter the hours in the Vacation pay column, leaving the other columns empty.
11. Click Preview payroll and then Submit payroll.

For more detailed information, visit this article: Create and run your payroll.
This approach ensures your employee receives their vacation pay in a separate check for easy tracking. If you need further assistance, feel free to reach out. I’m here to help you make this process as smooth as possible. Have a great day!