The Register Customer Payments page will open showing all Open Customer ledger entries. Select the Payment Made checkbox on the lines that you want the payment to be applied.
Notice that as soon as you select the Payment Made checkbox, the line will be updated, the Remaining Amount field will become zero and the amount will be transferred in the Amount Received field.
You can edit the amount received so that it matches the actual payment amount. Also, the Date received field will be updated with the work date, but you can change that to reflect the actual payment date.