Let me share some clarifications about entering invoices in the Self-Employed (QBSE) version.
The invoices you mark as paid doesn't automatically show as an income in the system. You'll need to add the payment from the Transactions section and categorize it as Business or Personal.
There are two ways to upload transactions in QBSE. You can either connect your account and download bank data automatically or import them via CSV.
To categorize, please follow these steps:
Go to the Transactions menu.
Find a transaction on the list.
Select Business or Personal.
Review the category in the Category column. QuickBooks tries to categorize transactions for you.
If you need to change the category, select the category link.
Select a general type, and choose a more detailed category.
I've also included some articles in case you need some ideas about how to record income transactions in QuickBooks: