If I owe the Fed and am getting a state refund, do I have to make a payment OR will the payment automatically be taken from my state return?

The federal government and the several states operate cooperating, yet parallel tax systems. While information is shared between the IRS and state taxing authorities, the assessment and collection of taxes, and refunding of overpayments generally finds the IRS and the states each staying in their own lane.

If you owe taxes to the IRS, you must pay the IRS. If you owe taxes to a State, your must pay that State. Each issues their own refunds, as well. The only common exception to this is the Treasury Offset Program, through which federal and state agencies can collect past due child support, past due taxes, and past due student loans by having money taken from any federal payment, including a tax refund, that you might be expecting.

In your current matter, be sure to pay the IRS before midnight, Monday, April 15, 2019.