I have a TrackIR + track clip, CH flight sim, CH pro pedals and Saitek Cyborg Evo force.
Of all of the above i only had to configure the pedals because they act as a joystick (x and y axis), but they do this in every sim i have tried them on.
Arma 2 had great joystick support, i'm sure ArmA 3 will have even better joystick support.