Hi jamie10,
I'll be happy to guide you in submitting your return.
We’re still developing an option to submit a Flat rate return in QuickBooks. Until then, you can continue preparing your VAT return, but you may need to use our bridging solution to file it to HMRC. This keeps you compliant while you’re still able to use all of QuickBooks functionality.
The bridging solution feature will import the amounts needed for boxes 1-9 from a CSV file, and you can then submit the return digitally from QuickBooks. Please can check our this article for your reference: Submit a VAT return through bridging software in QuickBooks - MTD for accountants.
If you have other questions, you can always go back to this thread. Thanks!