Hi austins8
We do not directly support the VAT apportionment scheme, you will have to do the calculations outside of QuickBooks and use the bridging tool, when it becomes available, to submit the return to HMRC in accordance with MTD.
To set up your banks within QuickBooks you will need to go to the banking section within QuickBooks, select add account and follow the prompts, you will have to do this again to connect the secondary account.