The 10% Early Withdrawal Penalty is automatically included in your tax return and tax due (or reduces your refund). It will break out and show the 10% penalty separately on your return (schedule 2 line 6 which goes to 1040 line 23). Then you get credit for all the withholding taken out on 1040 line 25b.
If you take a distribution from your retirement account, you will receive a 1099R in late January or early February, which must be entered on your tax return. That document will show how much tax was withheld and will indicate if it was an early distribution. The software will do the calculations and determine if you had enough tax withheld or if you owe more. You do not pay the 10% early penalty as a "separate" fee.
To enter your retirement income, Go to Federal> Wages and Income>Retirement Plans and Social Security>IRA 401 k) Pension Plan Withdrawals to enter your 1099R.
The 10% Early Withdrawal Penalty is automatically included in your tax return and tax due (or reduces your refund). It will break out and show the 10% penalty separately on your return (schedule 2 line 6 which goes to 1040 line 23). Then you get credit for all the withholding taken out on 1040 line 25b.