If the feature is activated (see how here), your customers can go on the Customer Portal.
Select one or several invoices on the "Invoices" tab
Click "Apply now" on the "Credit Notes" tab
Your customer can double-check their request and click on "Send request"
Once the request has gone through, you'll get a notification on the customer's timeline. You can either apply it in your ERP or reject it (see how here).