Ya, cool. Check BFD3's mixer page then and read the manual to find out how to change the channel ouputs (if set up correctly you will see the tracks within SONAR). I only have BFD Eco so can't help you there but the process should be similar (as it is with most multi out synths).
Also I made a typo/mistake. I meant to say that without setting up the synths channel outputs in this manner they will usually only feed the synths "Master" output into one track (or multiple tracks) inside the DAW. Thus offering absolutely no separation of the kit peices or ability to add effects/pan/generally mix said individual peices.
As you do this though keep in mind Stereo Mic Pairs (such as overheads and/or Room mics) should be kept in sync but as a "mirror" image of each other so you may want to keep those pairs outputting to a single stereo track so effects and volume levels are even. Otherwise if you use MONO tracks for those pairs make sure as you mix you preserve that "stereo pair" correlation (like keeping the levels the same, applying the same effects in equal proportion to both tracks, panning in equal amounts opposite of each other... stuff like that).
If you go the stereo track route but don't like the stereo panning of your Room/Overhead mics then adjust the pan positions within the sampler/synth mixer instead of trying to screw with that in Sonar which is impossible without some silly shenanigans.
Just my experiences.
Not a "pro".
Cheers.