Controlling the linear pots of an RC transmitter from Arduino

You probably need to explain the design of the "engines" in a little more detail. Are the engines electric motors, or are they actual heat cycle engines? Just thinking, you might use an resistor/capacitor circuit in the normal RC pot control (or speed switch circuit) such that when the pot/switch is moved the actual output voltage to the RC transmitter board very slowly increases and decreases slowing the final motor response.