No matter where you prepare your 2018 state return, you would indicate in the appropriate place that you had an overpayment from 2017 that you applied toward 2018 state taxes. When that's done, and if on the 2018 return there is still a net overpayment amount, then you could either choose to either receive that net 2018 state refund in full, or to apply part or all of it towards the next year's (2019) taxes.
Did you already file a 2018 state return this year? If so, did you not indicate that you had an overpayment from your 2017 state return to apply?