Your customers can pay for orders with a credit card on the portal, but you can also process payments on the CRM side. By default you can process Credit Card, Cash, or Check payments through the Process Payment Wizard in CRM. Payment can be processed for any active order or invoice.
Navigate to the contact record the payment will be from.
In many cases, the payment is for that person's orders, but you can pay any order from the process payment wizard, so you want to start with which contact the payment record needs to be linked to.