Hello there, lorraine-rossite,
QuickBooks values your data security. With this, I'd suggest contacting the ATLAS dedicated support team to verify if they still support the QBO integration process. From there, they can assist you on how to transfer your invoices from ATLAS to the program.
Once transferred, run the four reports below before you submit the VAT return. This ensures your tax figures are accurate.
If you're already using MTD, go through this article on how to file your VAT return: MTD for Small Businesses.
I'm just a comment away if you need further assistance. Have a great day, lorraine-rossite.