You would like to charge an order already in the system that was purchased by check with a credit card.
Click on Reports -> Orders and click the order number to 'view' the order in question.
If you have the credit card information for the customer, you can simply click the Charge button at the top of the page. 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, if you do not have the credit card information you can 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.