08-24-2009, 10:12 AM
The "correct" file structure is whatever works for you.
The only things you don't want to mess with are the System and Library folders, and the name and location of the User folders. (If you need a different account name, create a new account in System Preferences and delete the old one.)
Aside from those files folders, you are absolutely free to move, rename, Trash, change the icons of, and otherwise mutilate your files as you see fit. (Except in Texas, where they've passed laws about this, but anyway.)
Sometimes, a program will stop working if you move certain files that it wasn't expecting you to move. That's okay. That's how you learn about things. (A Time Machine backup helps here.) Other times, programs will re-create files that have been moved or deleted that they can't find.
99% of the time, again excepting those files used by the System, it really doesn't matter what you do with your fiiles.