How can we compliantly convey a payment in the following scenario?

Our organization makes a proprietary EMR technology tool available to our contracted primary care providers for use during evaluation, management, and general wellness visits.  The tool surfaces up-to-date, personalized data on the member pulled from across the healthcare ecosystem to the provider, for use during the patient visit.  The information provided in the proprietary tool is designed to help providers in early disease identification, intervention, and the closing of care gaps.

Pursuant to the terms of our Provider Agreements, our organization remits payment to participating providers within 10 days when complete and accurate information is submitted and received through our proprietary tool pertaining to a member visit.  The provider also submits a claim according to normal practice.  The EMR payments generated by using our proprietary tool set forth in the Provider Agreement replaces the Fee For Service payments for specific CPT Codes (i.e., the provider submitted FFS claim is paid at $0) when our proprietary tool is used in connection with the patient encounter.  The EMR payments generated by using our proprietary tool are processed through our claims platform and payment is sent to our clearing house through the standardized 835 process.  To identify the contracted payments generated by using our proprietary tool in the 835, we currently use certain non-standard CPT codes (997CA, 998CA, and 999CA).

We, therefore, respectfully request guidance on the following question:  Given that the codes we are currently using are nonstandard, how can we identify these EMR payments and compliantly represent them in the 835 transaction? 

Additionally, given that our contracted EMR payments may differ based on place of service and other factors, we request guidance on how we would account for those differences.