Why is there another 10%? Are you under 59 1/2 and taking a distribution? You can send in an estimated payment on form 1040ES or pay the estimate directly here
https://www.irs.gov/payments
Even though you have withholding taken out or pay an estimate it is not actually the tax. You will still 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 and the taxable amount on 4b. The withholding will show up on 1040 line 16.
If you have a 10% Penalty....It has to break out and show the 10% penalty separately on your return, (Schedule 4 line 59 which goes to 1040 line 14)
Then you get credit for all the withholding taken out on 1040 line 16.
