You may need to select the box that says "My form has other info in boxes 1-18" on the 1099-MISC input screen since Federal Income tax withheld would be reported in Box 4 and State tax withheld would be in Box 16.
When you enter the 1099-MISC, the tax withheld (Federal and/or State) flows into the program and will be accounted for when figuring the tax paid.
You will see the Federal tax that was withheld included on your 1040 line 25b.
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