NEW to DJM900 and CDJ 2000 Nexus setup to record

Hi, I just have a few questions on how to record with CDj2000's Nexus and DJm900 mixer. Ive been using Traktor s2 and Traktor 2 since April and i've recorded all my mixes on there without any problem. Ive just recieved my new gear mentioned above and I was having trouble being able to record with Traktor 2 using the new stuff. I seem to get Traktor to use decks 1 and 2 but both tracks will only play on one fader which is A. I know it might be a stupid question or maybe because im new id defo need some help with setting Deck 1 for fader A and Deck 2 for fader B! Thanks!