This is how my set up works with engine / autorotation set to throttle channel 3(engine).

This is the reply when asked the question from AFP chief programmer:-

Dear Neil,

Did you use the EXPERT settings or the EASY SETTINGS?
To set up your radio with aerofly pro?

Independent throttle and pitch only works in EXPERT setting!

In EXPERT setting check if the MOTOR channel for the helicopter
(Not the MOTOR 1 to 4 for the airplane!) move correctly if you
move your channel 3.


regards,
Torsten Hans