I initially opted to pay my state due with my federal refund. This costs $40. I switched options to pay with credit/debit. How do I get the $40 off total?

You misunderstood.   You cannot pay your state tax due from your federal refund.  The only thing you can choose to pay with your federal refund is the fee for using TurboTax to prepare your tax returns.  If you choose to do that, you will pay an extra "refund processing fee" of $40 ($45 in CA).   If you make that choice, your federal refund goes first to a third party bank.  The bank takes out your software fees and pays TurboTax, keeps the $40 for itself, and then sends the rest of the refund to you.  To avoid the $40 fee and the involvement of the third party bank, you need to pay your TurboTax fees upfront using a credit or debit card before you e-file.

 

REMOVE REFUND PROCESSING FEE

 

https://ttlc.intuit.com/turbotax-support/en-us/help-article/intuit-account-billing/remove-pay-refund-fees-turbotax-online-change/L7UxC6ZZp_US_en_US?uid=m6r4xelq

 

 

And----if you owe tax due to the state:

 

You must pay your state tax due using the state’s preferred method of receiving payment.  For most states that will be by making a payment to the state’s own tax website, or by mailing a check or money order.

 

 

https://ttlc.intuit.com/turbotax-support/en-us/help-article/state-taxes/contact-state-department-revenue/L9qVToi02_US_en_US?uid=m6e06um0

 

Also At the end Turbo Tax just shows you the net federal and state combined. But that is only for your info. You will still get the full refund and you need to pay a tax due. 

Check the printout or PDF of your return; look for the state cover sheet with the Turbotax logo.  If you owed tax, it will show the payment information and how/when you decided to pay.  Read the state payment instructions carefully since most states cannot be paid from within the TT system and requires additional steps.