RPM adjusts prop RPMs. Engine rpm's are basically irrelevent. Most props are connected directly to the output shaft of the engine, so both would be the same in those instances.
On something like a 109, I beleive they used gears going from the engine driveshaft to a cog on the prop hub, so there would be room for the hub cannon. Same type of thing for the P39. Once geared, you coudl have the prop and engine running at different speeds, but I'm not if this was done.
On a constant speed prop you have no direct control over the pitch. You set a certain rpm, and the prop will move to keep that rpm. I'm pretty sure most (if not all?) planes in AH had this type of prop in real life. I'm not certain tho.
On a variable pitch prop, there might be 2 or 3 settings you can choose from, but the prop wont adjust itself to keep a certain rpm. You would have to watch for overspeed and such in this instance. I believe someone mentioned that early spitfires had this setup.
AH treats every plane as a constant speed prop. If you keep the rpm setting at its highest, the prop will go as fast as its design allows, if there is enough power from the engine.