You can set the flight modes and channel used in the Full Parameter List and bypass the GCS GUI.
As for the flight modes used, it all depends upon your needs. During testing phases, I would add more QuadPlane flight modes to test hover and sensors like the BARO and GPS. My initial transitions were always QSTABILIZE to FBWA and back. I later added CRUISE mode to test the AS sensor. Next flying season, I'll continue with QRTL and AUTO mode testing.