Hello there, @nunhead_man.

You'll set up the VAT agencies as vendor in your QuickBooks. When recording VAT returns, you have to tag or account it to the corresponding agency (vendor).

For future help with VAT concern, you can refer to this link: QuickBooks Desktop VAT e-filing & Making Tax Digital.

Let me know if you have other questions with VAT by commenting below. I'm still here to help you more.