Every time I use a different drum kit - whether stock or made from cells I drag into Battery 3, I always split each cell off to its own audio outputs, set each cell's relative volume to some reasonable starting point, and save the kit off as a custom kit.
I then set up a track folder for drums in Sonar, with a single midi track for all drum data, and separate audio tracks for each kit piece, insert track icons, give them all appropriate names, etc.
I then create a main drums bus, and additional sub-buses for toms, cymbals, snare, etc.. that all feed the main drums bus, which itself feeds the master bus.
I then save all of the above off as a track template, in a drums track template folder, for later inclusion in future projects.
I have some stock setups for commonly used instruments in Kontakt, that have things like, Piano, Organ, Strings, Bass, and all of the audio and midi tracks, and that will get saved as a track template as well. I have track templates in Kontakt for entire strings sections, and brass sections, as well.
Hope that helps,
Bob Bone