I think you mean you received a W-2 form that reported federal income taxes withheld from the gross wages reported on the form. If so, they would be reported in box 2 on the W-2 form. When you enter them into TurboTax on your amended return, they will show on line 12 of the amended tax return Form 1040-X. As such, they will be applied against your amended tax along with any other federal taxes withheld to determine if you owe additional tax or will receive a refund.
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