I have already paid the state tax owed. Will the total amount of 3978 federal return be deposited into my checking account?

[xmasbaby0]

It is not possible at all for the state tax you owe to be deducted from your federal refund, so assuming there are no other offsets to your federal refund, you should receive it.  If you requested to have TurboTax Fees deducted from your federal refund, that will be done by a third party bank and you will receive the rest.

Did you choose to have TT fees deducted from your Federal refund?  (Remember that if you did that, you also agreed to an extra refund processing fee of $39.99)

How can I see my TurboTax  fees?   

https://ttlc.intuit.com/questions/2565973-how-do-i-review-my-fees-in-turbotax-online