You can record a credit for a customer or a payment made in the customer credits page.
Here you can do two things:
1. Assign credit to customer account. This can be to handle instances such as giving customer a referral discount
2. Manually record a payment not associated with an invoice.
The main list shows credits that are available for customers as well as you can add new credits.
This will bring up the payment form. Here just fill in the details and click on add payment to save the payment for the customer.
Credits will be automatically applied when a new invoice is created.
Manually use credits
If you want to apply credits to an invoice that has been already created you can manually apply credits to it. Go to the Invoice and select to add payment for it. In the dialog box that open to record payment you will see a button to use the credits. Credits are applied one at a time. So if you have multiple credits in the system the steps have to repeated.