After you file

I stand corrected ... however you either need to make the override in the FORMS mode of the downloaded program  OR   make a manual correction on line 16 (and recompute the rest of the form)  on a paper filed return if you mail it in or use the online program  OR  just send less with the amended return (or pay it online and not with the amended return)... the IRS will marry up your payments with the return automatically.