How do I change Form 1040-X Line 16 (Total amount paid with request for extension to file, tax paid with original return, and additional tax paid after return was filed)?

Add the amount paid after filing  to the  extension payment in the TT program ... 

To enter, change or delete a payment made with an extension request (Federal, State, Local) -

• Click on Federal Taxes (Personal using Home and Business)
• Click on Deductions and Credits
• Click on I'll choose what I work on (if shown)
• Scroll down to Estimates and Other Taxes Paid
• On Income Taxes Paid, click on the start or update button

On the next screen select the type of extension payment made and click on the start or update button

                                                                                                                                     
Or enter federal extension payment in the Search box located in the upper right of the program screen. Click on Jump to federal extension payment

@Critter-3 

We hope your procedure will propagate such a revision to Form 1040-X if an AMEND is in progress.

It should.

You can't use this procedure if you are e-Filing (now closed) because you will be

changing the "payment with extension" line. That's not what the OP said.

@james2c19v 

When paper filing 1040-X,

do not include your old 1040 nor your revised 1040 because the Form 1040-X reflects any changes there and becomes your new tax return.

If the program thinks you sent the entire payment then you may not be able to change this in the program  so you may need to manually change line 16 and the rest of the return as well.   Or you can file it as is just knowing you did not send the full payment and either send what you really do owe now or wait for what should be a refund as the IRS will automatically recompute the bottom line for you.