Reply to HELP! Hooking up Traktor Scratch Pro 2 + DJM 900 + CDJ200's

Ok I just switched from serato scratch live to Traktor Scratch Pro 2. First off the gear I have is DJM 900 mixer, 2 CDJ-2000's, Mac Book Pro, Traktor Scratch Pro 2. I bought the Traktor Scratch Upgrade since it works with the DJM 900 Mixer. This is what I want to do. First I dont always use a lap top so I would like to be able to use regular cd's when ever I want. I also use Rekordbox (usb stick) What is the best way to hook up my set up? Right now I have a Lan switch with the CDJ's, Mixer, and computer hooked up to it. I also have usb from the two cdj's going to the mixer. Lastly I have the digital cable going from the cdj's to mixer. There has to be some way to use CD's, Rekordbox, and Traktor with out all the cables. How can I use CD's Rekordbox, and Traktor with out all the cables all over the place? I am not using a X1 controller so I am wanting to make my CDJ's native to traktor. Second part is how do I make Traktor Scratch pro 2 native to my cdj's? I found the video on how to set up the mixer but I didn't see how you got to the very first screen to change the settings http://www.youtube.com/watch?v=bspD_Hxi-4M. I don't have any idea how to navigate through Traktor so please be as spcific as possiable when explaining.

Setting up my music:

So after I get this all set up how do I sort my music? In serato I had different crates for each genre. On Traktor I didn't see how to do that same type of thing. Sorry I am sure alot of this is super easy to some of you but your help is appriacated.