The Reconcile Accounts button on the Account Management Search screen provides you with a list of customers where there are payment transactions that are not directly tied to an order or refunds that are not tied to a cancellation.
By clicking on the spyglass icon, you are taken to the customer's reconcile account page where you can click the green plus sign icon and associate or reconcile the transaction to an order (just select the correct order from the dropdown list).
The Auto Reconcile button will automatically associate transactions to orders if all the necessary information is available to the system.