I think one has to get away from the idea of putting things in permanent containers. It is much better to create associations between items using metadata. We had a whole discussion about this sort of thing in another thread:
http://forum.eastgate.com/t/user-attributes-or-tags/1069
The point is that agents allow you have have dynamic “containers” that present you with the stuff you want, and it doesn’t matter where the original is. You don’t need to spend time and effort “filing things” in the “proper place” because you find it according to what the note says, or its metadata, not according to where it resides in the structure of the database.
Not sure if that is clear, but perhaps the other thread will make it clearer. As I said, you have to get away from the idea of using this program like other programs.