Are you saying that the IRS took your State Refund? How did you determine that? Is it possible your State Refund was used to pay your TurboTax filing fees? If you didn't previously owe the IRS for back taxes, and you filed requesting a Payment Arrangement, they would not normally take your State Refund. If you did owe back taxes, though, they may have, but you should receive a letter from them to that effect.
If you have already filed and your return has been accepted by the IRS, you can't change your Payment Method. In this case, if you elected to make payments on Federal Tax due, you will receive a letter from the IRS confirming your payment arrangement. If you pay your Balance Due at that time, you won't need to make any further payments to the IRS.
Here's more info on IRS Payment Options.
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