I'll provide additional details to clear things out about your concern with the unapplied case payment income in your Profit and Loss report, @JPWelter.
You're doing great on following the steps provided by QuickBooks Online. You don't need to worry about the unapplied cash on the report, as no action is needed. Thus, the report you've pulled up serves as a running balance.
This means when you record the expense, the amount shows as negative, but this does not need to worry because this was already offset, and balances were zeroed out. That's why, when you go to the customer's account, the invoice shows as paid and closed, and nothing shows as unapplied.
You'll want to review these great resources to help you modify your reports based on the information you need, as well as how to save its current customization settings:
Keep me posted if you still have questions or QBO-related concerns. I'll be around for you. Have a great day.
