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W-4 Wages and 25% Flat Tax on Supplemental Wages in same payroll

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I am processing taxable fringe benefits and regular wages in my April payroll. The fringe benefits are considered supplemental wages and taxed at a flat tax rate of 25%. The regular wages are taxed using the individual's W-4. Upon review of the calculations, it appears that all wages and taxable fringe benefits are being taxed using the W-4 and the 25% flat tax rate is being ignored. I've calculated the amount that I expect the tax to be for the fringe benefit, but the actual tax is about $50 less. When running a payroll, can both methods of taxing be used or does one take precedence over the other?

We are on GP 2013 R2.

Thank you for your help.

Tammy

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