The IRS only processes your federal return, not your state return. The IRS does NOT get your state refund. Your state refund cannot be used to pay a federal tax due. You must have misinterpreted the "summary" give after your return was filed that showed the net difference between the tax due and your refund.
You must pay your state tax due using the state’s preferred method of receiving payment. For most states that will be by making a payment to the state’s own tax website, or by mailing a check or money order.
https://ttlc.intuit.com/questions/1900884-what-are-my-options-for-getting-my-state-refund-or-for-pay...
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