How to control hybrid drone-rover system?

So we are building a hybrid drone rover system that can fly and move on the ground, we have four BLDC motors for drone operation, four geared motors for ground and two servo motors operating the transformation mechanism. I can see us using a pixhawk to control the BLDC motors or the DC geared motors separately, but what we want to achieve is that when we flick a switch on channel 5 of our transmitter, the servo motors should operate and the operation changes to aerial or ground, accordingly. How do we go about implementing this? Do we build custom firmware? If yes, what files am I looking for? Does mission planner or other gcs have inbuilt stuff to handle this? Will python scripting for mission planner work?

The idea of 2 Flight Controllers has been discussed before using the Stand-by Mode feature. Not specifically for your use case but perhaps relevant. One running Copter, the other Rover. Servo multiplexer perhaps…
It has nothing to do with Mission Planner.
Stand-By Mode

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Nice! Thanks for the quick reply! Also, say if I were to upload custom firmware, by building through WAF and that whole procedure, i was thinking i could implement some algorithm like - if I get a val on channel 5 of RC, then I trigger the servo motors, and use the firmware from Rover, or from ArduCopter, in accordance. Can this be done?

Not on 1 Flight Controller I don’t think. But, it’s not my area of expertise.

You might be able to use the QuadPlane firmware and adjust that firmware to your needs.