When you take the withdrawal you don't pay the actual tax on it. You have taxes withheld like from your paycheck. The withholding is just an estimated amount. At the end of the year you will get a form 1099R to enter into your tax return. The withholding will be in box 4. On your tax return you enter the full amount as income. Then you get credit for the withholding on line 25b.
You still have to enter the whole gross original 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 or 5b. The withholding will show up on 1040 line 25b.
