I have 2 Primes (Cable Card), and to HDHomeRun (OTA). I only use the OTA for major networks such as NBC, CW, CBS, etc. So what I did is grouped the OTA tuners for those channels with the corresponding channels on my cable feed, and set the OTA channels as a higher priority. That way, if I run out of OTA tuners, it will still fall back to the cable card for recording.
Been doing it this way for years with JRiver, and it works great. Of course, I am one of the lucky ones where my cable is 'copy freely'. If your cable is Copy Once, then JRiver won't support your Cable Card.