OK - up at the top of your Kontakt UI window, there is a button for Output Section. Click it, and it will display the output channel defaults Kontakt sets up for you.
By default, Kontakt will route each loaded instrument to the same ST1 output, as you know.
What I do is to get all the desired instruments (4-5 is around the max I will put into a single Kontakt instance), into an instance of Kontakt, then I will go down to the Output Section, and there are some Batch Functions with a drop down, and one of those is to Clear all outputs and create one stereo output channel for each loaded instrument. Click on that batch function, and it will do just that.
Now, while this next bit is purely for my own desire, as you see, the default is to cram parts of the Instrument Name into the name at the top of each channel, and it looks like crap to me. SOOO, I double click on each Channel Name in the output section, and rename things more sensibly, like Piano, Bass, Organ, Strings, Lead, etc....
Once the above is done, it is time to set the routing assignments for midi tracks and audio tracks to pick up the right pairings for each loaded instrument in the Kontakt instance.
So, for each given instrument from the Kontakt instance, assign the Input to a stereo audio track (or pair of mono) to pick up the appropriate OUTPUT for that given instrument from the Kontakt instance.
Then, make sure the associated midi track for that instrument is also pointing to the correct Kontakt instance, AND (this is important), you will need to set the Midi Output Channel for that midi track, to match the midi channel for that loaded instrument in the Kontakt instance. (Kontakt will auto-increment midi channels starting from 1, for each loaded instrument, so if you have Piano, Organ, Strings, Lead, and Bass, those will receive on midi channels 1, 2, 3, 4, and 5, respectfully). For the midi track, you will find the parameter for setting Midi Output Channel on the channel strip for that midi track, just under the FX Bin.
Completing the above for each instrument and each instance of Kontakt will have it all rocking and rolling. If you leave each midi track's midi INPUT set to omni, you will still hear the appropriate sound when you play, because as long as you have the desired instrument's midi track in focus, and the midi input set to omni, the setting of the Midi Output Channel will result in you sending the correct midi channel to the Kontakt instance, and the desired instrument will see midi data on its midi channel and produce sound, which gets sent back through the appropriate audio tracks for one big hootenanny.
I hope the above helps, please let me know if you need me to take another stab at it.
Bob Bone