When you have submitted a VAT Return, you will either pay HMRC or they will pay you the balance of what's owed from that VAT Return. The balance of what's due will sit against category 8302 - 'VAT - HMRC'.

When this money has been paid/received through your bank account, you will need to ensure you allocate this bank entry as a Money In or Money Out (depending on the direction of the money), and code it to the same category as mentioned above (8302 - VAT - HMRC), with a tax code of non-Vatable.

See the example below of a HMRC receipt: