Taxes owed on a 2020 federal amended tax return, Form 1040-X, cannot be paid by direct debit from your bank account using the amended return.
You can only pay the taxes owed by check mailed to the IRS with a payment voucher, Form 1040-V, or use the IRS payment website for Direct Pay - https://www.irs.gov/payments
You will not be charged twice. You correctly made the payment on the IRS website.
