For those following this thread or looking for an answer in the future, I got the solution from TurboTax Support. Here it is: you re-open your TTax filing and go to the section where Estimated Payments are listed. Beneath the standard Quarterly payment boxes, there is a link to "Add Addtional Payment." There you enter the payment that you made -- in my case the credit card charge that was processed with my first filing transmission. This immediately changed the tax due in my filing to the balance of what I owed rather than the total tax calculated as if I hadn't made the first payment. The filing then went through, the balance was charged to my same credit card, and the return was accepted by Federal and State.
