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
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.
20% is the minimum mandatory withholding on a distribution like a pension buyout paid to you that is eligible for rollover. You can request that the payer withhold more. If the forms for requesting the distribution do not allow for requesting more, you can submit Form W-4P to the payer to request additional federal withholding:
https://www.irs.gov/pub/irs-pdf/fw4p.pdf
If the distribution has already been made with only 20% withheld for federal taxes, you can make a federal estimated tax payment as suggested by VolvoGirl. Similar things can be done with state withholding or estimated tax payments.