You would like to charge a credit card for an order already in the system, but not yet completed. Or perhaps you had your system set to manual processing but now have a payment processor integrated, and you want to know how to charge the stored credit cards and complete the orders.
Click on Reports -> Orders and 'view' for the order in question. At the top of this screen, you will see a Charge button. Click the button, confirm/edit payment details, and press Charge. Once the order has been successfully processed, the Order Status will be changed to Complete.
Alternatively, you may want to send a Payment Retry Link to the customer, which sends an email to the customer allowing them to edit their own payment details and resubmit.
NOTE: This procedure does not work with PayPal. More information here.