The correct way to log a pre-payment in QuickFile is to assign it direct to the supplier or client. There’s a brief guide on this here. The guide outlines it for a client, but the process is almost identical for a supplier.
So what you would need to do is go back and untag the pre-payments of £200.00, and re-tag them using the steps in that guide above. This will then add the amount to your supplier’s account ready for allocation to an invoice.
As they wouldn’t have been claimed on previous VAT returns, the system will then pick it up on the next return for you. I would still double check with your accountant however regarding the return. While I can’t see it being an issue (seems you would have paid more to HMRC previously), it’s always better to be safe than sorry and check 
Hope that helps