Add em into iTunes, and then iTunes to "Consolidate the Library" - It will automatically sort everything out. But then you'll have the MP3z in two places, but you can move em out of iTunes once they are all consolidated, and then move it anywhere ya like.

Actually I have thousands of MP3's and they are all in my iTunes Library, lately it has been behaving well. I used to meticulously sort em all out by Artist Name/Album Name/Song Order. So I leave em in iTunes and use the Library Sort features to find what I'm looking for.