Payments to HMRC for VAT aren’t normally issued against an invoice.
What happens is when you submit your VAT return in QuickFile it will post a liability to the VAT account (Nominal ledger 2202), you can view this by looking at your Chart of Accounts.
Now later HMRC will debit your account for the VAT owed. When you see this on your bank statement in QuickFile you would tag it from the bank as a payment for VAT and QuickFile will make another posting to nominal 2202 to reverse the previous entry created from the VAT return.