For most people, letting iTunes organize files is easier.
However, folks like myself prefer not to have iTunes organize files because we use files from various sources. I use directories that reflect origin of files then folders within that represent the music collection (CD's as example). Others might organize strictly under Artist.
Example directories -
CD Converted to Apple Lossless
iTunes music purchase
iTunes audiobooks
iTunes Movies and TV
CD Audio Books
Flac converted to Apple Lossless
Misc MP3
As for ease of handling, it really isn't a big deal because I simply do "add to library" as I get new music after I put the file in the correct category. (I leave the copy files unchecked under preferences). Given that I store my files along with other media directories, I can differentiate rather quickly what belongs where. (I also have 96/24 flac files, 48/24 5.1 flac files etc.)
Again, for most people letting iTunes handle it all seems to be the easiest.