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You enter the withholding when you enter the 1099R for the distribution.
Enter a 1099R under
Federal Taxes on left
Wages & Income
Then scroll way down to Retirement Plans and Social Security
Then IRA, 401(k), Pension Plan Withdrawals (1099-R) – Click Start
Don't type the bank name or try to import it.
At the bottom pick - Change How I enter my Form
Then on the next screen pick - I'll Type it in Myself
Be sure to pick the right kind of 1099R on the 4 boxes. 1099R or CSA1099R or CSF1099R or RRB1099R
If you are filing a Joint return be sure to pick which person it is for.
And You didn’t actually pay the tax or the 10% penalty (you pay a 10% early withdrawal penalty if you are under 59 ½). You had taxes withheld like from your paycheck. You still have to enter the whole gross amount (before taxes were withheld) with your other income to figure out the total tax (and it may put you into a higher tax bracket) and then the withholding is subtracted from the total tax to figure your refund or tax due. The Gross amount shows up on 1040 line 4a or 5a and the taxable amount on 4b/5b. The withholding will show up on 1040 line 25b.
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