How to run the middle payroll with a different amount than half of the salary? The advance salary we pay is not half of the compensation.

Hello steve-safoundation,

Welcome to the Community. I'll be glad to provide the info you need so you can manage your work with peace of mind. QuickBooks offers the right tools and resources that allow you to get ahead with your accounting. 

Based on the details you've share above, I recommend running an unscheduled pay run as that's used to pay employees outside of the normal pay schedule. Here's how you can do this: 

1. Navigate to the Employees or Payroll menu, then select Employees.
2. Click on the ▼ dropdown, and choose one of the following options: Bonus only, Commission only or Fringe benefits only.
3. Select As net pay or As gross pay, then select Continue.
4. Enter any info about taxes or paycheque calculations (if applicable).
5. Select or review the QuickBooks Bank account to track your payroll, the pay period, if applied, and Pay date.
6. Select the employees you'd like to pay.
7. Enter compensation, memos, or any other paycheque info as necessary.
8. Hit Preview payroll.
9. Select Preview payroll details, Save for later or Submit payroll.
10. Confirm the amounts and payment methods and select Finish Payroll.

I encourage you to try this out and let me know how you make out. I'll be one message away in case you have other questions. Otherwise, I wish you a great rest of the week.