Had a problem before where i ended up duplicating lots of tunes on my player.. and im not sure how i did it (duplicates of songs in the same playlists)

Probably had Windows Shortcuts or M3U files pointing at the songs as described here.

You don't need to worry since the "duplication checker" happens before synch time. You drop the files onto Emplode, it tells you what was a duplicate, then you're free to dig through the tree and check to make sure you didn't add anything you didn't want to add before you actually hit the Synch button.