@J > Due to the limitations of there only being one return channel from the mixer to the software, you're out of luck for at least using the 1200's as timecode controllers for Traktor. You could certainly set it up so the 1200's are just for playing vinyl and the 2000's / X1 bring audio from Traktor into the mixer.
All you do is run the Setup wizard (found under the Help menu) and tell it you're using NO timecode and CDJ2000's as controllers. It will default them to decks A and B, and it may default your audio interface to the DJM2000, but you can check that within the settings.