The pathfinder tool can also be used to divide overlapping shapes as well as unite them.
For example, as PrintDriver mentioned, a final logo should be built as efficiently as possible without overlaps. The pathfinder tools can help remove those shapes that are behind other shapes by dividing up the shapes where they overlap and allowing you to remove the pieces that aren’t needed.
The best way to get used to how it works is to just draw a bunch of overlapping shapes, then experiment with what the various pathfinder tools do with them.