Paradigm has an option to automatically charge Credit Card Fees on Sales transactions.  To turn this on, go to:  System > Company Preferences > Sales > Bottom-right corner for “Default CC Markup” and select the value.
These values come from the list of standard discounts/markups that are set up in System > Company Preferences > Setup > Standard Discount Selection > Setup (button).  To create a CC markup, you need to create a negative discount as shown below.
This makes it so that when you pay a single invoice by credit card via the “Receive Payments” popup before it is posted, the CC Fee is automatically calculated and added to the “Other” field on the invoice.
If there is a dollar amount other than zero in the "Other" field when you "Receive Payment" via credit card, it will display this message.
If a customer is exempt from CC fees, then go to Accounts Receivable > Customers > Detail > Credit and Terms and check the "CC Fee Exempt" box.