@Cameron > Are you using the DJM900 as your main audio interface for the computer, and if so, are you expecting the rekordbox software to output separate channels? Because if so, it doesn't do that.
While yes, you can use the DJM's built-in audio interface to output audio from your computer's various software applications, including DJ apps, rekordbox is NOT designed as a DVS meaning it is for managing your song collection and previewing mixes, as well as acting as a source for audio files when linked with CDJs. You can't use it as a "live" DJ software such as Traktor, Serato DJ or Virtual DJ. Please consider a different configuration or software for this purpose.