Ahem. Here's what happens;

If you boolean -

Case 1)
The piece you're trying to cut the larger piece with appears to be a single sided, thin piece (simply a distorted plane). If that's the case, a boolean difference will leave you with only one half of the model, due to normals (that is, unless it decides your normals have problems, and produces some error - such as if the plane goes only partway though the piece). To counter this, duplicate the shape you want split, as well as the piece doing the splitting. After splitting the first shape, click on the shape doing the splitting, and click on Edit Polygons > normals > reverse, and then simply do a difference again.

Case 2)
If the piece doing the splittingis not in fact a simple plane, but is actually a distorted box (however thin otherwise), a boolean difference will simply put a hole down the middle - the two sides will still be one piece. To finish this one, click on Edit polygons > seperate. So long as these two pieces don't touch each other, they'll be seperated into two distinct shells (of course, so will anything else that might have been otherwise connected to them)


If you use 'Extract faces'
Selecting contiguous or adjacent faces and extracting will seperate them in one contiguous piece (by default; you can tell it otherwise). Do not move the manipulator if you do so, because it'll effectively make like an 'extrude faces' action, potentially causing problems (depends). This unfortunately also only allows a change in geometry that is actually there - you'll only be able to effect the actual (current) ouer shell of the piece. Oh, and it won't cover over the resulting hole left from the split, either (well, you can tell it to duplicate what you just took off, but that's a little pointless here....


Erm, any other questions?