"Do I need to subtract the tips from Qualified Wages if the S-Corp is passing along the credit for Social Security and Medicare Tips (call this credit SSMT) to the shareholders (changing the Qualified Wages amount) or will the SSMT credit be subtracted from the Employee Retention Credit in the 941-X?"

I think you are mixing apples and oranges. Wages and Taxes are not the same thing.

The FICA Tip Tax Credit allows employers to take a credit on a portion of the employer FICA taxes paid on the employee tips. If the business is a pass-thru entity, the credit will pass through to the business owners on IRS Form K-1 and the business owner will take the tax credit on their individual income tax return. The credit is only allowed to offset income tax liabilities and cannot offset employer payroll tax liabilities.