After you file

When I filed my amended return, TT asked me how I wanted to pay what I owed my state. I chose to have it deducted from my bank account on May 17th. Then I get a letter from my state stating I need to pay the amount due by May 17th, either by check or online. If I pay online directly to state, will TT also deduct from my account on May 17th? I don't want it deducted twice.