I'm still way down on Blender 2.72 learning curve. I've tried to get an answer just working with a basic cube and a plane and I'm not getting the expected result.
Object mode>select cube>shift select plane>modifier (boolean difference)> select cube (again)>apply
At this point, I would expect to see three objects: two pieces of the cube and the plane. However the plane is apparently fused to a piece of the cube and the other object is the original cube.
Accepting this result and another bunch of commands and I might get to my result. Do I really need to do this? Have I overlooked a very simple answer? BTW, I'm expecting the two pieces of the cube to be manifold.
I've spent a lot of time searching, but I can't seem to find the magic keywords or phrasing.