I had been granted an extension on my federal return (used form 4868) so I should automatically have an automatic 6 month extension for my GA Return.

I did not know that I had to use form IT 560 and submit a check to pay tax due and I instead just submitted a credit card payment with Official Payments Corp.

I later on read the instruction booklet which stated "Credit cards are not accepted
at this time for payments associated with extensions, amended returns, or installment payment agreements."

In this case how should I go about filing my return. Should I submit IT 560 with my return? My situation is further complicated by the fact that I am waiting on an ITIN for my spouse which I will not receive before the extended due date of Oct 15th. In this case will I have to pay late filing penalties since I cannot file before Oct 15th?

Thank for your help.

Determine your GA state tax liability and IMMEDIATELY make a payment for that liability PLUS 10% (you are already late, so interest and penalties are due).

When you finally CAN file, explain the problem and ask that any late filing penalties be waived. Interest will still be due, but it is only 12% annually.