I appreciate you for coming back to the thread and adding extra details about your concern. I'll be sharing details on how adding tax agency works in QuickBooks Online. Then, I'll ensure you can manage your VAT accurately.

Setting up a separate 'Tax Agency' and making this filing will be treated separately in the software and won't have any negative impact on current UK registration. Additionally, you can add a group rate to combine multiple taxes and make applying them to transactions easier. All taxes you include are calculated and charged at once but we track them separately for you.

You can click this article to see extra details: Set up and edit VAT settings, codes and rates.

Lastly, you may refer to this article to see different details on how QuickBooks Online automatically calculates VAT when you make a sale: Learn how QuickBooks Online calculates VAT.

Please don't hesitate to click the Reply button below if you have other concerns related to QuickBooks. I'm always around to help, LDOLMAN96. Have a great day!