I’m glad to see you here in Community, @blackoak88.
Let me give you an insight into what's going on.
In QuickBooks Self-Employed, invoices are exclusively used to track expenses. They don’t reflect directly on your profit & loss, and tax reports. That’s the reason why your invoice has a different amount to your income totals.
What I can suggest is to carefully track invoice payments under the Transaction page. Utilize this article for your guide: Manually add transactions in QuickBooks Self-Employed.
On the other hand, you can also track sales tax in QBSE, however, they won’t be visible on the reports. The same way with an invoice, you have to track them to Transaction reports. See this link for your reference: Manually track sales tax in QuickBooks Self-Employed.
Don’t hesitate to drop your comment below. Have a wonderful day!