If you want to run a report to see if payments are applied to invoices and what invoices they are applied to then run the Payments Applied report.
You can choose a date range to/from, and select a Payment Status including All, Unapplied, Partially Applied, or Fully Applied.
Once you run the report you will see all payments and the invoices they are applied to including the Amounts Applied and Amounts Remaining.
You will also see the Unapplied payments. You can click on the Payment which will bring it up in a pop-up which you can easily Edit and apply to an invoice if there is one out there. Once saved, refresh the report and the payment or credit adjustment will show as Applied.
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