When you mark your VAT return as filed, QuickBooks Online automatically creates a VAT due. If you've paid the liability to HMRC, you can record the VAT payment by following these steps:
On the left panel click Taxes, and click the Returns tab.
Under Filedreturns, click the Recordpayment link.
Select the bank account you've used to pay HMRC.
Choose the PaymentType, and enter the PaymentDate and Payment amount.
Add a Memo if needed.
Click Save.
Once recorded, a transaction will be created on your books which you can match from your bank feed.
For more information about VAT returns and payments, you can check these articles: