Nah, what you need to do is go into Preferences, go to the Advanced tab, and make sure check "Copy Media to Itunes Folder" or something like that. That way whenever you play a song, or import something, it'll automatically copy it into the folder and it won't be lost. You won't have to worry about organizing individiaul files in folders...
I used to keep my music folder extremely organized, but when I stopped using Windows Media Player and got an iPod, I realized there's no reason for me to worry about the folder when Itunes would copy everything to it's own folder. Now I just import the CD I downloaded, let itunes copy it, then delete the folder. SIMPLE!