I wanted to pay my state taxes separate from coming out of my federal

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State taxes owed can NEVER be paid from a federal tax refund. Choose the option in the File section Step 2 for paying the state taxes owed.

Well you are in luck ... the state balance due can NEVER be paid with the federal refund... that is not even an option in the FILE tab. What is probably confusing you is the SUMMARY screen which only shows the NET affect of the federal refund and the state balance due ... that is informational only.