When customers have credit memos available, they can be applied in a few different ways.
Applying credit memos
With these options, manage which invoices to apply credits to, and in some cases, how much credit to apply.
From the Credit Memo Actions menu
When charging a customer - Click Apply to automatically apply any available credits
When creating or editing an invoice - Enter the amount to apply from the available credits
When a customer logs into the Customer Portal to make a payment, they will see any available credits, which are automatically deducted from the Amount Due.
Your customer chooses when and how to apply available credits
If your customer is paying you from a Basic Payables account, they'll see Apply vendor credits under Payment Options, when vendor credits are available. From there they can choose how much of the available credits to apply.