Personally, I would have used the tax agency websites to make the payments if I had any doubt they would be debited properly with the software.

Would have taken way less than an hour of my time speaking with Intuit about it.

Serves me right for thinking it was going to be a 2 minute phone call turned into "May I put you on a brief hold?"  I also had to resolve the reject for filing an extension after the due date for the other states. Guess Intuit was surprised.