Hi there, @kitzy1. I'm here to lend a hand. 

QuickBooks allows you to adjust your VAT return before you submit it to HMRC. Since we can't recommend an adjustment account, I suggest you coordinate with your accountant. 
 

For the payment that was made outside QuickBooks, you can create an expense account and choose check or expense transaction for the payment.

See the screenshot below for your reference. 

You can read through this article for more details: Make VAT adjustments in QuickBooks Online

Nonetheless, if you already enter the historical transaction, you can record the payment in the tax section. Let me show you how.

1. Go to the Taxes menu. 
2. Choose the VAT tab. 
3. From the Returns section, locate the returns you've paid. 
4. Click Record payments from the Action columns. 
5. Enter the VAT payment details.
6. Click the Save button.

Let me also add this article that you can read for future reference in submitting your return: Submit a VAT return to HMRC using MTD in QuickBooks Online

If you have other tax concerns, let me know in the comments below.  I'll be sure to get back to you.