I tried to set up the "standard configuration", which means that the base station is connected via USB to your PC and the 2nd board (rover) via UART to the GPS port. In this case, QGroundControl will detect the base station, starts a survey-in procedure and receives the RTCM data needed at the rover.
Then QGC transmits these RTCM data as MAVlink messages via your telemetry link (f.ex telemetry) to your pixhawk (TELEM port). So this data link is the only one you have in this configuration!
At the end of this RTCM-data-chain your pixhawk will forward the RTCM data via the GPS port to your rover. That's all...
There are 2 things why you have to turn off the onboard radio of your C94-M8P modules. First because they are not needed
But furthermore, you have this one UART1 on C94 modules, which is connectet to onboard radio by default. If you want to use this connection via J8 pin header, you have to make sure, that nothing than you speaks with this port!
This configuration insures, that QCG and your pixhawk know what they have to do. It's a plug and play solution.
PS: There is one funny fact i can't understand so far - although the QCG and the pixhawk do the configuration, one of my boards didn't want to be the rover (independent on firmware and initial config). So i used that one as the base and the other one as rover - so please cross check this!
A short reply would be great!