I appreciate you coming back to us for additional support, steve-leyland. Allow me to join this thread to add more insight about recording your VAT payment in QuickBooks Online.
To make sure it won't duplicate with the ones that are added in your books, I'd recommend you undo the transactions from your bank feeds. Here's how:
Once undone, you can now go back to the Taxes page and record the VAT payment. Then, follow the steps provided by my peer @MirriamM to match the transaction from your bank feeds.
For future reference, here's a great article you can refer to in managing your VAT returns: Submit A VAT return in QuickBooks.
Feel free to visit again if you have additional questions. I'm always delighted to help you some more.