By saving credit cards, you increase the level of payment flexibility. Your customers don't have to enter their credit card information over and over while you can automate payments.
To use a credit card on file to capture payment.
Click on "Receive Payment" as you would normally do from an invoice or the customer profile
Select "Credit Card" as the payment type
Click on the "Process Payment" toggle to reveal the "Card on File" tab
Select the credit card to use for processing
Click on "Apply Payment"