Go to A/R>>Receive Payment.

 Use the available filters to find the order or the customer to apply a credit card payment.

 Enter the payment amount, the date and in the Payment method drop-down menu, select Credit Card Web.

Click on Apply action, for the specific order you want to pay (Notice that there is a button called Auto Apply Payment which will automatically apply the payment amount entered starting with the oldest invoices).

Click on Pay & New. The system will open a screen to enter the credit card information and the billing information. Notice that if there is card already saved, you will be able to select it.

Click on the payment amount and wait a couple of seconds until the payment is processed. 

A confirmation message will appear.

Once you close the confirmation window, the system will take you to the Receive Payment screen and will clean the payment information.