The 46 is much smaller. It's considered a medium lift helicopter. The 47 is a big boy. It's considered a heavy.
The CH-46E is operated by the Marine Corps. The CH-46D was operated by the Marine Corps, but is now only used by the Navy. The MC is in the process of retiring all of it's CH-46E's, and the Navy's CH-46D's are probably all replaced by H-60's.
The Various versions of the CH-47 are operated mainly by the Army, but the Air Force has some speciallized CH-47/MH-47's.
The CH-46 Sea Night and the CH-47 Chinook are about as different as a Pinto and a Mustang. It may not be appropriate to replace one with the other, but don't forget the cardinal rule, Build your model your way.
Semper Fi,
Chris