In the amendment interview there was a screen that asked if you had paid the balance due yet ? If you missed it then the easiest way to make the correction is manually ... print the 1040X and put in the correct amount on line 16 then simply recompute the rest of the form yourself.
If you're familiar with TurboTax and working directly with Forms, then this is the procedure: (I do not know how to get the Step-by-Step interview to ask you for this information.)
1) back up your current file in case this hoses it up (if you did not yourself think to do this, then consider carefully before proceeding)
2) switch to Forms (click Forms, upper right-hand side (RHS) of the Step-by-Step window)
3) open Form 1040-X (click on it in the LHS pane, or click on Open Form and enter 1040-x)
4) scroll down to Line 16 (you can't edit it manually)
5) right above Line 16 is "Original 20XX Return Payments Smart Worksheet" and you *can* edit the amounts in that
6) edit the choice that applies to you (A or B or C) by clicking on the number currently displayed
7) enter supporting details if desired (click on the '+' sign to the left of the amount displayed)
😎 verify that now Line 16 shows what you think it should and print out Form 1040-X to make sure you're happy with it (click 'Print Center', upper RHS, above the Step-by-Step icon in blue, then Preview Print Copy)
9) save the return if this fixed it, or cancel out of all the preview stuff and go back to the Smart Worksheet to try again.
(You can exit out of Forms by clicking on Step-by-Step, upper RHS, where Forms was when you first started this whole thing.)
Hope this helps!