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You can create an Expense transaction to record the payment you've made to HMRC for the VAT Return filed outside of QuickBooks. I can walk you through how to do it.
First, let's make sure to create an Expense account and use it in tracking the VAT payments. Here's how:
- Go to the Accounting menu.
- Click the New button.
- Choose Expenses for the Account Type.
- Select Taxes Paid for the Detail Type.
- Enter a Name (i.e HM Revenue & Customs) for this account.
- Click Save and Close.

Once completed, you can create an Expense or Cheque transaction to record the VAT Payments.
- Choose the New (+) icon.
- Pick either Expense or Cheque.
- Select the VAT agency from the Payee drop-down.
- Enter the necessary information.
- In the Category details section, choose Taxes Paid account for the Category, Description, Amount, then select No VAT for the VAT column.
- Click Save and close.

On the other hand, you can follow the steps below to record VAT payments in QuickBooks:
- Go to the Taxes menu.
- Choose the VAT tab.
- From the Returns section, locate the returns you've paid.
- Click Record payments from the Action columns.
- Enter the VAT payment details.
- Click the Save button.

I'm adding this article to help you manage VAT in QuickBooks: Submit a VAT return to HMRC - MTD for small businesses.
Get back to us here if you have other questions about tracking your VAT-related transactions. I'm always here to help.