The payment process for original e-files and amended returns are separate. Furthermore, the amended return processing takes 8 to 12 weeks - perhaps longer in tax season. So even if you mailed the amended return today, the odds are not good that the IRS would even have it before the payment date you set in April.

Speaking of which, did you set a date for a direct debit in April? If so, there probably isn't a way to change it, but you can call the IRS at (800) 829-1040 and ask.

You will have to bite the bullet and pay the extra amount for the original return and then hope the refund of the difference on your amended return does not take too long.