I was going to write a short guide on the subject (but I don't understand everything and I did not want to simply copy & paste info here) so I found 3 good guides for you to read on the subject.
I will however, discuss the directory that I am the most familiar with. The home directory. When you open the home directory you see a directory with your username, it is similar to the
C:\My Documents if you were using Windows 98
C:\Documents and Settings\Username if you were using Windows XP, or
C:\Users\Username if you were using Windows 7
The home directory has sub directories:
Contains your desktop shortcuts
Make sub directories to fit your needs and save your Word & Excel (or Writer & Calc) and other documents here.
The folder your web browser downloads to by default that you are supposed to sort regularly, but seldomly do (well, me at least). Files are meant to stay here short term.
Put your mp3, ogg, aac, wav, flac, aif (or whatever format you use for your music) files here.
A place to save all those lovely tux wallpapers and lol cat pictures you have been collecting. Cut & paste them here from the Downloads directory now ;)
Also a good place for storing your photos from your digital camera, etc.
Used for sharing files over a network.
Save your templates files here. Lots of programs like LibreOffice, Scribus & Inkscape use templates.
Remember to make sub folders here, otherwise things can get a bit messy.
As you can see the folder structure is self explanatory, and you should not have any trouble with it. Remember that it is dangerous to mess around in folders that you don't understand what they are there for.