As long as iTunes is not set to organize your library, scanning your computer for media will just add entries for each file to the iTunes database. When you add new music outside of iTunes, you can rescan folders to have iTunes pick up the changes, though tag changes outside iTunes can be difficult to get picked up and moving files around will cause iTunes to lose track and have to be fixed, sometimes painfully.
As an organizer, iTunes Doesn't always play well with others.
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