Your post is simply not clear. If you purchased the CD/download, you paid for it before you even downloaded or installed it. The only additional fees incurred with the download would be if you added another state program, add-on features like audit defense, or if you e-filed a state return and had to pay the state e-file fee. You could pay those fees online using a credit or debit card before you e-filed, or you had the option to pay the fees from your federal refund---which would also cause you to have an extra "refund processing fee" and allow a third party bank to receive the refund first. Not sure what you are referring to when you say you had to "log in separately" to pay filing fees.
Exactly what fees are you being asked to pay?
I apologize. I purchased the download from Amazon as I have for many years. The fee is for filing the state return. Every year that I have used TurboTax to efile, I have always been asked to log in to my TurboTax account when it was time to pay the State filing fee. This year the screen for payment opened within the TurboTax software, which has me concerned as I expected the extra step. I am trying to find out if this is the expected way for the payment screen to act in this year's version of the software.
When I filed my state I don't remember if I had to log into my account again. I think I did. I make lots of notes when I file and for state I said Pay for Efile $20-10 =$10. And I wrote down my username and password. I got an Order confirmation email.
You didn't happen to pick the wrong button to have the state efile fee deducted from your federal refund? They changed the screen this year for that.