When you select to pay your Federal taxes due by credit card, and you elect to pay the balance due by credit card at a later date, you are instructed to visit https://www.payusatax.com/TaxAct to make the payment.
The payment is made on a separate website from the TaxAct website. payUSAtax is a service of Link2Gov under agreement with the IRS and is certified as an IRS payment processor which allows taxpayers to make a payment by credit card for taxes due to the IRS.
Since you are prompted to pay prior to completing the filing steps, if you did not continue on and complete the filing of your return (completed on the screen where you select the Submit button), it is possible the payment would be completed but the return was never actually filed. In these cases you may receive a notice from the IRS stating they have received your payment, but not your return.
If you need to file your Federal return (because it was not actually filed with the IRS the first time), but do not need to make a payment again because you have already completed the payment information and submitted the payment on payUSAtax.com, you would select Mail a Check as your payment option and then just not mail the check since the payment has already been made.
Note: It is ultimately the taxpayer's responsibility to ensure the payment made on the payUSAtax.com website was processed.