I paid for my turbo tax fees from my refund and was deposited by a third party bank will the third stimulus check go to my main bank account on file with the IRS

There has been NO INFORMATION on what was JUST PASSED yet  so you will need to wait and see what is going to happen.  

Either the third party processing bank will get the stimulus money and pass it thru like the refund  or they will not and the IRS will mail you a check.  Until something is posted on the subject no one knows.