I'm a newbie (I hate that word) to Linux, myself. I just barely started using it, and have found that the file structures can be somewhat confusing (though I really don't pay too much attention to it). However, in this regard, I have to admit that old habits from my Windows experience are creeping in here. For me, I have already split up my home folder into a Downloads folder (from which I then further split into specific folders for each program), a Documents folder (akin to My Documents) wherein I keep all of my music files, word processing files, etc. I have found that by following this practice, my top-level folders stay extremely clean. Things get messy the further down you go, though.
I'm not sure there's a "best practices" method for organizing your folders. Come up with a system that works for you, and that's how you should do it.