At the end, going over my way to pay. Why does my "total refund" subtract what I owe from my state taxes? Are they going to pay them for me?

[JudyTR]

This is just a review of your overall taxes.  If you owed both Federal and State, you would see the total amount due.  Same goes if you were received a refund from both Federal and State.  Your State taxes will not be paid with your federal tax return.  You get to choose how you pay your taxes owed and using your Federal return is not one of the options.