If you really want to understand everything, purchase the very extensive and nice Lightroom tutorial offered on this site.
(disclosure: I have absolutely no vested interest, direct in indirect, in that purchase - I just bought and liked the Lightroom 2.x tutorial) There's also a tutorial called "Where The #%*! Are My Pictures?" that seems perfectly tailor made for your case (but I haven't seen it)
If you aren't interested, simply remember that Lightroom isn't a file system explorer/manager. It is essentially a database manager that contains pointers to your pictures, thumbnails, and a lot of other info about keywording, edits etc... what you see in the library isn't necessarily connected to what happens at the file system level. You can have a completely different organization at the file system level and at the library level, although both will converge if you use exclusively Lightroom to import files. As far as I am concerned, my organization is a total mess. I import pictures using 6-7 different programs on 5 different computers. On a roughly yearly base, I try to reorganize everything and consolidate all pics on one of my 2 NAS. At that point, I add all the pictures that haven't been edited (on the 3 computers I never use to edit stuff) to the NAS and simply reimport everything ignoring duplicates. I am of course a bit more careful with the two computers where I have edited files in Lightroom as I want to keep my keywording and edits. For that purpose it is RTFM, watch a tutorial on what you can/should do etc...