No payment options will go through when you amend your return and e-file. When you e-file your amended return, you need to either mail in a check with a payment voucher (1040-V) or you can go on the IRS and/or State website to make your payment.
IRS payment website:
https://www.irs.gov/payments
If you owe State taxes, you can go on your State's website for their payment options.
