I create one track with the VSTi loaded on it, add a MIDI event and do all my programming in the one MIDI track. Then I usually manually create tracks for Kick, Snare, Tom 1, Tom 2, Tom 3, Overheads, Hihat, Ride and Room. Then in the SSD player I make sure all those parts of the kit are routed to their own set of stereo outputs (like for kick go to the output configuration screen and create an output routed to Plugin Output #1 and Plugin Output #2). I usually delete all of the preconfigured outputs (st. 1, st. 2, surr 5.1 1, surr 5.1 2, etc.) because having outputs named after a surround setup seems dumb as hell to me, so I create all new outputs named after the drums that are routed to them.
You have use the 32 out Kontakt player to have enough pairs of outputs for all this stuff and make sure the VSTi track is set to a 32 channel multitrack in the Reaper I/O options.
So now say it's setup like this
Kick: plugin output 1 and 2
Snare: plugin output 3 and 4
Tom 1: plugin output 5 and 6
etc.
Now on the new tracks you created for each drum, create a send from the VSTi track that sends the right channels tot he new track. So kick would be 1/2 -> 1/2, snare would be 3/4 -> 1/2, Tom 1 would be 5/6 -> 1/2, etc. I route all the cymbals in the player to the one stereo output called overheads just to make it more like mixing a real kit.
I'm at work and don't have SSD installed here but setting up the room is a bit weirder I think, the SSD room by default is routed to Aux 1 and NRG is to Aux 2 or something and I can't remember how to change that off hand without it in front of me but hopefully this helps.