Yes, if you have gone the entire way through your tax return and are ready to file, the penalty for underpayment is included in the final amount due to the IRS.
You can see this by clicking on Tax Tools on the left-hand side of your screen, Tools>>> View Tax Summary>>> then look at your Estimated Tax Penalty. You can also look at line 79 of your 1040 or line 51 of your 1040A.