Music Folders - Root, Samples, Stems. iTunes

I just realized that I have 4500 tracks and 4-5 of each song. I'm trying to get all my music in to one place with no dupes.

A few questions about file locations area of Preferences...

1. Is there supposed to be any music files (mp3, wav) in the root folder? Does Traktor look at sub-folders?
2. What is supposed to be in my Samples folder? I've got a hodge-podge of things like a Beyonce album stems, and several folders named after genres like Trance and Techno.
3. Are stems supposed to be in a specific folder?
4. How do I prevent Tracktor from using iTunes? I've tried to change it to an empty folder and it switches it right back. I think it's even looking at music on my iCloud too which I don't want.

I don't have any folders in the list on bottom so all those songs are coming from the other paths in the file locations screen.

I also saw in a google search that I should be able to scan for dupes but I don't think it works the same now. My Traktor software is up to date but right clicking on the tree doesn't give the option. Check consistency looked for missing files as far as I can tell.

Will clearing my collection fix it? Seems kind of drastic but at this point I'd prefer to rebuild if I can clear all the dupes. I can import my existing music to playlists through the Explorer. If I can use my folders correctly it should make keeping them organized easier in the future.

I appreciate any help you can provide.