We charge a variety of ways depending on the client and the service we are providing. If we are doing a complete service, submitting, followup, denials, patient billing, etc, we do a %. But if they only need to have the claims submitted, no followup, then we do a per claim. Some clients we have set up on a flat monthly fee (their request).
If you are doing followup it definitely works better (for us anyway) to do the %.
Michele