I run about 5-6 instruments max per instance of Kontakt 5, and never ever use simple instrument tracks. They just do not work for the multi-timbral synths, from what I understand.
So, especially for Kontakt, I use separate audio tracks and separate midi tracks for each instrument, and use the Kontakt Batch Functions in the Output Section to set up separate stereo outputs for each loaded instrument, then insert audio tracks and midi tracks for each instrument in the Track Pane in Sonar, and route accordingly back to the corresponding instruments in Kontakt.
To take the above even farther, for common combinations of loaded instruments in Kontakt, I will select the audio and midi tracks for that instance of Kontakt, then create a Sonar Track Template, which will save off all of the audio and midi tracks I set up for that instance of Kontakt, as well as the multi-rack and the loaded multiple instruments and their settings in Kontakt, all as part of that track template.
Then, for new projects that use the same or similar instruments, I just insert from the saved Track Template, and all of the routing assignments, tracks, and the Kontakt instance, are all loaded into the new project with just a small number of mouse clicks.
VERY handy.
Hope the above helped - please post back if you have any questions about any of it.
Bob Bone