You can make it so you only see the collections and the books that aren't in a collection only. These directions are for the DX, but I would guess it would be similar on a kindle 2. When on the home screen, press up until the line that says "Show all * Items" on the left and "By title", "By author", or "By most recent first" is highlighted. Press right on the joystick, and you'll see several options, go over and select "Collections" and then press the joystick down. Now you should see all your collections on the top of the home screen, and any books/magazines that aren't categorized underneath them. The books that are in a collection don't show up anymore.
One note is that the order the collections show up in this mode is by most recent first. That is the last collection you went into will be at the top, the second last collection will be the second from the top and so on.
Hope this helps!