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. Using the buttons at the top of the order page you have two options.
Email Payment Retry - To notify a customer of an Incomplete order you can send a Payment Retry Link by email allowing them to edit their own payment details and resubmit.
Charge - If you have the credit card information for the customer, you can simply click the 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.