Any underpayment penalty is likely already being included in your federal tax amount due. You can tell the program to have the IRS bill you the penalty amount later, but the default is to include it with your amount due on the return. You can check to verify the penalty is on your return by looking at Line 79 of your Form 1040 (or line 51 if filing a 1040A) - that is where the penalty would show. The line for the penalty is below the amount you owe, but it is included in the number above. If there is no penalty there, then that means the IRS will calculate the penalty and send you a bill for you to pay.
