Are my underpayment penalties being included in the Federal Tax Return due amount, or do I need to pay that separately?

Yes, any Underpayment Penalty you are assessed is included in your Federal Tax Due amount.

 

You'll see this on Form 1040, Line 38 and on Form 2210.

 

Here's more info on the Underpayment Penalty. 

 

 

 

The penalty on line 38 is already included in the tax due on line 37. You don't have to pay it separately.   And it is just an estimate so it is possible for the IRS to recalculate it and send you a refund or a bill for more.