You deal with the 1099-R under the Personal Income tab in the Retirement & Social Security Income section. Elect to start/update the sub-section for 1099-R and enter the 1099-R exactly as printed. there "WILL" be boxes in the program for entering taxes withheld. You just enter the 1099-R into the program, exactly as printed and the PAY ATTENTION to the screens that follow. If you don't read the small print, you very well may be surprised at all the penalties the program will say you have to pay. So please read everything on each screen before making selections and proceeding to the next screen.
When you enter the Form 1099-R, you'll enter the amount in box 4 of the Form 1099-R into box 4 of TurboTax's 1099-R form. TurboTax will include this tax withholding on Form 1040 line 64 or Form 1040A line 40 along with withholding shown on any other Forms 1099 or Forms W-2.