Great info - I happen to also do a couple other things, after loading the desired instruments into a given Kontakt instance:
 
1) In the Kontakt instance, at the top is a button to toggle on/off the display of the Output Section.  I make sure that is on, so that I can manipulate things in the Output Section.
 
2) By default, even though Kontakt will automatically increment the midi channel by one, every time another instrument is added - it will assign all the outputs to the ST1 main stereo output channel.  Since I want individual control of each audio output from each loaded instrument, I run one of the Kontakt Batch Functions (you will see this down in the output section) - I expand the Batch Options and run the one that clears all outputs and creates one stereo output for each loaded instrument.  This will do just that.
 
3)  The one downside of the above is that it renames each output channel to some strange mashup of the instrument's name.  SO, the simple fix is to double-click on each Output Channel name, and change it to something easy to read, short, and simple, like Piano, Rhodes, Organ, Violin, Bass, etc.  This makes setting the input assignments for each of the audio tracks simple - just match the audio Piano track(s) to the Piano output channel from the appropriate Kontakt instance - either Piano Stereo, or a Piano Left and a Piano Right, etc.
 
I hope that helps - it took WAY longer to reread what I typed above, than it would take to actually DO the above steps, but I wanted to try to explain it properly.  :)
 
Bob Bone