The best way to set it up would be to use a MIDI cable and plug it into an external sound card, which is then connected to your computer via USB.
Remember MIDI only sends 1 way signals and controls the software. Therefore you will not use the outputs on the DJM-800 and you will need to set the audio to come out of the external sound card via a selected channel.
I don't have the DJM-800 MIDI documents Pulse provided, but you should be able to find some online by googling or ask another member such as Pulse if he has it.
You can also google more information on MIDI usage and capabilities to find what would be the best set-up for you.
In my opinion, if you have 2 external CD players or 2 CDJ's, I would personally use the DJM-800 as a stand alone mixer with the players. You can connect the players to Traktor if they are USB enabled, or use Traktor Scratch Pro (1 or 2) to control the audio. But I would definitely use the DJM-800 as the DJM-800 and not to control Traktor. Why? Because the DJM-800 is/was the industry standard DJ mixer for the past 5+ years and sounds amazing on it's own with all it's built in effects, color effects, 3 band EQ... everything on it is amazing to use. If you use it to control Traktor, then you are using the software mixer built in to Traktor, meaning your DJM-800 is just a controller and you're not using it for it's amazing sound quality.
Also, I think the built in mixer in Traktor isn't that great at all. I've played around with it and I think the software still has a way to go before I consider giving up the true hardware aspect of it.
Hopefully someone else sheds some light on their opinion so it's not so one sided. lol
Hope this helps.