The federal tax withheld should be in box 4 of the 1099-R. You just enter it there. (If state tax was withheld it would be in box 14.) But on your tax return you report the gross distribution, not the net amount that you received. And the 1099-R box 1 and box 2a show the gross amount. The 1099-R does not shoe the net.
The tax withheld will be included in the amount on Form 1040 line 25b. That's where it gets accounted for and applied against your tax for the year.
(This is similar to your W-2. Box 1 of your W-2 shows gross wages, before any tax that's withheld. And you report the gross wages as income on your tax return. The federal tax withheld on your W-2 is reported on Form 1040 line 25a.)
