My employee advance pay is not in the total wages in Box 1 of the W-2

You'll want to review your payroll item list, mickey7.

The box for Federal Withholding might have been unchecked. Once reviewed, let's go ahead and create a payroll liability adjustment to correct this.

Here's how:

1. Go to the Employees menu. 
2. Choose Payroll Taxes and Liabilities.
3. Select Adjust Payroll Liabilities. 
4. Click the Prev Adjustment button to look for the adjustment you created. 
5. Modify the Effective Date.
6. Click OK. 

Let's run the Payroll liability balances report to review the adjustments. 

I'm always available if you need anything else.

Thank you!