There is RPM increase/decrease for each engine...you just have to select the engine first.
I have 2 knobs on my throttle that rotate and push in...I have one knob as engine 1 and the second as engine 2...and I have another button for all engine. So I press the appropriate engine and rotate the knob it will only affect the one engine, then if I press all engine button both rpm can be controlled.
Hope that helps, I can go ingame and see exactly how I've set it up, if not