Multiple Instrument Tracks sharing one VST?

You need to split those instrument tracks into an audio track and a midi track for each of the instruments you wish to have loaded into that Kontakt instance (this would be true for any multi-timbral soft-synth, and not just Kontakt).
 
Once you do it a few times, it will be second nature to you.  :)
 
What I do is:
 
1) Insert an instance of Kontakt into the Synth Rack - Usually, I select the one that has support for 16 audio outputs.
2) Load desired instruments into the Kontakt instance, I limit the number of loaded instruments in a single Kontakt instance to 5-6.  Please note that as you add each instrument, Kontakt by default will auto-increment the midi channel associated with each newly-loaded instrument, which you DO want.  Kontakt will also auto-assign the audio output of each of the loaded instruments to ST1, which is stereo channels 1/2 - which you do NOT want.  (That will get addressed further down in these instructions).
3) For purposes of this walk through, let's assume you loaded a Piano, Rhodes, Strings, Bass, and Choir, which will get assigned to midi channels 1, 2, 3, 4, and each instrument will send audio output to ST1.
4)  OK, now you want to fix the audio output channel assignments, so that each instrument gets its own stereo output channels.  There is a SUPER easy way to do this with Kontakt - first, make sure the Kontakt instance has the button for Output Section clicked, so that you can see the internal mixer within the Kontakt instance.  Down in that Output Section, click on where it says "Presets / Batch Configuration", and then click on the option that says "Batch Functions", and then click on the function that says "Then, under Batch Options, click on the one that says "Clear output section and create one individual channel for each loaded instrument". (It's way harder to type this up than to do the steps - almost done with this part, by the way).  Kontakt will try to mash the preset name from each instrument to become the name of each output channel, so like New York Grand Piano blah blah will get squished into NewYorkGrandBlah whatever.  I find those mashed up names to be rather hideous, so I double click in the name at the top of each of the output channels, and rename the output channels to stuff like, Piano, Rhodes, Strings, Bass, Flute, Violin, etc...... That makes things way easier on the eyes and brain. 
5) So, at this point, you have the Kontakt instance loaded with Piano on midi channel 1 outputting to a stereo audio channel called Piano, Rhodes on midi channel 2 outputting to a stereo channel called Rhodes, Strings on midi channel 3 outputting to a stereo channel called Strings, and Bass on midi channel 4 outputting to a stereo channel named Bass.  
 
After completing the above, for this walk through, the Kontakt instance stuff is done, and now it is time to get the audio and midi tracks inserted, named, and assignments made.
 
1) In the Track Pane, Insert the desired number of audio tracks needed for the instruments.  I choose to use both a left and a right mono track for a stereo output instrument, such as piano, because I frequently slightly process one side or the other differently - others use a single stereo track instead.  
2) Name the audio tracks appropriately, for me and this walk through, that would be Piano Left, Piano Right, Rhodes Left, Rhodes Right, Strings Left, Strings Right, Bass Left, Bass Right.
3) Set your panning however you wish for the above tracks.
4) For each of the above tracks, assign the Input to the appropriate output channel for that instrument, from the Kontakt instance, so Piano Left should have its input assigned to Piano Left (mono) from the drop-down list for the Kontakt Instance.  Repeat this for each pair of tracks.
 
Now, you only have to setup the midi tracks and make those assignments, and you are done:
 
1.  In the Track Pane, insert one midi track per loaded instrument in the Kontakt Instance.
2.  Name them appropriately - I would like use Piano Midi, Rhodes Midi, Strings Midi, and Bass Midi.
3.  Set the Output for each of the midi tracks to the Kontakt Instance the instruments are coming from.
4.  In the Inspector Pane, for each midi track, you also need to set the Midi Output Channel to the appropriate midi channel the corresponding instrument in the Kontakt instance is set to process to.  This is set by clicking in the drop-down immediately below each midi track's FX Bin.  For this walk through, the Midi Output Channel for the tracks would be Piano:1, Rhodes:2, Strings:3, Bass:4.
 
That's it.
 
Again, it takes far longer to explain it than to do it, and once you do the above a couple of times, you will just remember how to do it.  I also frequently set up a group of commonly used instruments, put the various tracks into one or more track folders, select the tracks and any buses and whatnot, and save it off as a Track Template.  That makes it a cinch to insert all of the above with just a couple of mouse clicks to tell it which Track Template to use.
 
I hope the above helps explain how to use separate audio and midi tracks for Kontakt.  There are additional considerations, such as gain staging, and going into each instrument in the Kontakt instance and potentially removing the default so that the instrument's volume as set in the instance will not be directly responsive to CC 7 or CC 11 settings.
 
But, I think I gave you the basics - and REALLY they aren't as difficult to do or any of that - it's just a pain to try to be thorough in typing them up.
 
Bob Bone
 
 
 
 

Trying to explain what to do is WAY harder than to actually DO the setup with an instance of Kontakt and multiple loaded instruments.
 
Basically it is:
 
Load Kontakt instance in Synth Rack
Load desired instruments into Kontakt instance
Assign each loaded instrument its own output channels from Kontakt
Insert appropriate audio and midi tracks into Sonar
Make appropriate routing assignments
Ta-Da
 
Bob Bone