For models with additional functions you will need a Radio with extra channel, or you can use not allocated channels.
If your transmitter has additional channels they must be calibrated at first. After that you can allocate them to the desired function in Aerofly. If you do not have an “extra” channel you will have to double occupy a stick.
For gliders it is no problem to use the throttle stick for the flaps because you do not have a throttle there. In motorized models it is more problematic. If there is no other way, allocate it to the throttle (full throttle – flaps retracted), not nice but it works