An entire section in the DJ Masterclass is dedicated to setting up and maintaining your collection.
Personally I keep all my music in a folder structure that makes sense to me. And I leave the tracks there when I enter them into iTunes (so not making automatic copies to the default iTunes location). It makes it easier to backup stuff or find stuff when I am not using iTunes for some reason (like on a CDJ setup).
I am sure some of our resident Traktor guru’s can tell you exactly how to get your track analysed in Traktor while still maintaining all the info and smartlists you made in iTunes.
Good luck and greetinx.