Hi Lee, thanks for posting on the Community. 

Creating a VAT adjustment would be the recommended way to account for exceptions on your first return in QuickBooks. If you don't want to do this, you can instead include the exceptions by creating a nil/dummy filing for the period prior to the start date of your current return. This will then allow the system to recognize any transactions dated prior to this as exceptions. 

To do this, temporarily disable MTD by clicking Edit VAT > Edit settings > Toggle off the slider for MTD > Save. After this, click Prepare return and amend the start and end date to a period prior to your current return. Check that the return contains no data, and then mark as filed.

Note: if you've already added the historical transactions with VAT in QuickBooks, you'll need to edit these to remove the VAT code (change the 'Amounts are' drop-down to 'No VAT' on each) before creating the dummy filing. Then, after marking as filed, edit each transaction again to add the relevant VAT code. 

You can then turn MTD on to sync your open return with HMRC's expected periods, and the historical transactions will show as exceptions.

We recommend working alongside your accountant if you need any support with this, to ensure the return is recorded accurately. If you don't already have an accountant, you can find one near you on our online directory.