I'm happy to provide more information about unapplied payments for you. This feature is to help business owners keep track of all the debts that aren't invoiced. The feature isn't something you can turn off due to it being a beneficial feature. If you want to import your Invoices from your other software into QuickBooks, so the payments have something to match, you can import them using a CSV file or check out our third-party app options.
Feel free to comment below if you have any other questions or concerns. Best wishes!