Hello,
QBSE doesn't function the same as QBO.
In QBSE, income is ONLY driven by the bank transactions. You would need to have a deposit into your account marked as Business Income in order for it to show as income on your reports.
Yes you can send invoices from QBSE and mark them as paid, but that has no effect on your income in QBSE. If the payment on the invoice has been entered or downloaded on the bank screen and you marked it as Business Income, then that invoice payment is counting as income.
Hopefully this helps clear this issue up for you.