I use a combination of the drum sampler's internal mixer and individual audio tracks. My standard template combines instruments into five busses within Superior Drummer's internal mixer that are then routed to five separate audio tracks:
Kick in, out and sub -> KICK bus in sampler's mixer -> Kick audio track (mono)
Snare top, bottom and comp -> SNARE bus -> Snare audio track (mono)
HH, OH -> CYMBALS bus -> audio track (stereo)
All toms -> TOMS bus -> audio track (stereo)
Ambience near, mid, far, bullet -> AMB bus -> "Room" audio track (stereo)
Effects are also a combination of the sampler's internal effects and track effects. EQ is done within SD2, and I often use the built-in transient shaper on kick, snare or toms. Compression and limiting are normally done in the track, since that's what's most likely to be tweaked after the drums have been frozen.
Part of my rationale for doing it this way has to do with my underpowered computer. SD2 is a big CPU and RAM eater, so the drums are typically the first thing to be frozen. Routing to separate audio tracks and using external effects lets me retain mixing options that would otherwise be frozen if I did it all within the sampler.