Once you submit a VAT return and it opens HMRC as an Agent, it might be you're using the Agent credentials which is used for the client's submission. That being said, if you use Your Books in QuickBooks Online for Accountant to prepare and manage your firm's VAT returns you must authorise QuickBooks to interact with HMRC with Your Books. This is a separate process to authorising QuickBooks to interact with HMRC for your client files. Please follow the steps below on how to enable the connection in your books.
Login to your QuickBooks for Accountant file.
On the left menu, click on Your Books.
Click on the Gear icon. Then, Account and Settings.
Select Advanced on the left menu, expand Making Tax Digital for your firm's books.
Select Learn how to connect and follow the onscreen instructions to complete the steps. Note: use your government gateway ID.
Once done, you can now submit a VAT return using your login credentials. Please click this article to see the detailed steps: Submit a VAT return in QuickBooks Online. You'll need to go to your Firm then, Your Books and Taxes tab.