You would typically enter the prepayment for that supplier so that it predates your bank opening balance. You would then need to adjust this amount out out the opening balance in the bank settings.
e.g.
You are setting your bank opening balances on QF for 1/12/2015, your current account open balance is £1000. At this point in time you have a credit balance with Ecotricity for £100. You would then enter a debit on your bank for £100 on 30/11/2015 (one day before the OB), then adjust the Opening balance up to £1,100.
