Back in the day, I tried to use iTunes for a while when I bought my iPod. One of the first things that it asked me was to take control of my music, as it would reorganize it by itself. I agreed, but tested it first with a small sample. When I saw the mess it had done to the way I organized my music, specially with the files' names, I backed out of the auto-organize option and preached heavily against it to everyone I knew.
I learned my lesson: never let whatever service control your files. And always, ALWAYS have backup. Remember: The answer to life, the universe and how many backups you should keep of your stuff is 42.