Can I manually enter a client's credit card after they order?

Yes, you can enter and run a credit card via your order page for any orders that were not paid at checkout if you are using ShootProof Payments, PayPal (Pro version only) or Authorize.net. 

On a particular order page, you will see the "Mark as Paid" link when there was no money collected from your client at checkout.  After clicking the "Enter Credit Card" link and entering the required information, the gateway chosen on your Accept Credit Cards page will be used to run the client's credit card for the amount that you enter.