We are in Southern California. We bill for a scenario similar to yours.
In terms of data entry, we enter the same data into the Practice Management software that we would enter if we were billing a normal Health Insurance carrier. This is for record-keeping in case anyone wants a history of patient visits, etc. This record keeping cannot provide complete data on CPT codes used for the reason in the next paragraph.
We get paid 5% on office visits (usually 99212 / 3) and sometimes for EKG's (93000) only. Any other work the provider does is noted on the fee slip, but we do not enter that into the Practice Management software and we do not get paid a percentage for that work. We also do not send patient bills for this provider's capitated patients (he has a mix of capitated and non-capitated).
Because the provider is being paid a flat fee for seeing the capitated patients, regardless of what CPT codes he uses, he codes the office visits on the lower side - so as to pay us less money, regardless of the work done. We generate enough revenue off of this provider to make it worth our while. Your mileage may vary.