I'm not a rocket scientist, but my understanding is that efficiency is derived from the exit velocity of matter from the engine. So the faster it can fire matter in the opposite direction the more efficient it is. There are some other factors as well like bell shape, which are generally designed to provide better efficiencies at different atmospheric pressures (ranging from sea level to vacuum of space). The main consideration after these factors is the mass of the engines. If multiple engines and one giant engine had all of these same factors equal, then I don't think there would be much difference in the efficiency of the rocket. Likely though, there are differences and other advantages to multiple small engines. The easiest one for me to think of is modularity. If you want a specific thrust for a payload it's much easier to add more small engines together than to try and throttle down the large engine to the correct amount, if that is possible at all.
