A customer can have unapplied payments on account for a variety of reasons. Some of the most common:

To apply an unapplied payment to an invoice, click on the hand icon in the grid. This will show a list of invoices available to apply this payment to. Simply select the invoices this unapplied amount applies to, and click confirm. The process is now complete.
If at some point, a customer has many unapplied payments, these can be merged into one for organization purposes. This may happen if a customer consistently pays over each month on their A/R payments.
Check the box next to each payment to be merged together. From the “With Selected” menu, choose “Merge” and click “Execute”.