Hello Claralacy, Thanks for posting on the Community page,
So QuickBooks self-employed is only a partial template for you to use for the self-assessment form that you fill out on HMRC website and then send it off to them.
you can run the tax summary report in QBSE and then copy the figures into the corresponding boxes for HMRCs online SA form.
The invoice section in QBSE does not affect in anyway the tax summary only the transactions section in Quickbooks Self Employed affect the tax summary section for you so it would be a case of manually having to add these transactions in for it to then show on your tax report.