@frankcalabrese76
When you enter your entire 1099-R in the software, you are also entering whatever tax withholding was done when you took the distribution. That is just a prepayment against whatever taxes/penalties may apply at the time you actually file your taxes.....just like you have withholding to pre-pay your income taxes on a W-2 form.
The Income tax software and forms will still calculate what the penalty was supposed to be (if applicable) , and your 25% of withholding will be added to all your other tax prepayments to be used against ANY taxes and/or penalties calculated on you full 2020 tax situation.
____________*Answers are correct to the best of my knowledge when posted, but should not be considered to be legal or official tax advice.*