Your experience is going to depend on how you plan to integrate the CDJ with Traktor. It will also depend on the rest of your setup.
Using the CDJ in Advanced HID mode is one way to go. By doing this you are simply connecting the CDJ via USB and it can control some of the functions in Traktor. This is somewhat of an alternative to using timecode discs. The downside is that Native Instruments has not yet fully added Advanced HID support, so the functions available are limited. (example: you cannot see the full track info and waveform on the CDJ screen) Serato has done a better job in this regard. Eventually, if NI adds full Adv HID support, then you will get all of the track info and waveform on the CDJ-2000.
Option 2: Use timecode discs. This will give you better scratch control than the current level of HID available on Traktor. But besides that, it's not really a benefit over HID control. You will also have to use a Scratch certified soundcard or mixer.
I will point out that many DJs prefer to just use the CDJ-2000s on their own with a mixer. It really makes life easy when minimize the setup complexity. A lot of top-level DJs have either avoided Traktor, or ditched it, because they like the simplicity of the CDJ-2000s on their own.