Can you reconcile Cash Advance to Deposit in AR?

We are looking at replacing a customization*, and were a little confused by the Cash Advance Reconciliation screen. It appears that they want you to put in check numbers to identify the payment was made by the employee, but that they don't give a way to link it to a AR deposit that was posted (our preferred solution). Is this accurate or are we missing something?

*Our current customization has several layers. Basically our organization is paying the statement balance in full for Travel cards (and will not change this). This means that when users make unapproved charges on the card they owe our organization. I characterize this as our organization unwittingly giving them a Cash Advance that needs to be returned. Currently our customization makes a receivable in AR that alerts us that the user owes us money, and clears when the payment arrives, but this is not how we want to handle the situation. We would like to have the Cash Advance be where