I never use Simple Instruments, but to the best of my knowledge, you cannot load multiple instruments into a single instance of Kontakt, when using Simple Instrument Tracks.
So, you may be burning through a bunch of memory needlessly - just be aware of that. As you get into more and more complex projects, memory utilization may become an issue.
And really, if you load let's say 4 instruments into an instance of Kontakt, it will automatically assign midi channels 1-4 to them, in the order you added them to the Kontakt instance. If you then use the batch function to configure each loaded instrument to have its own stereo outputs, rename those outputs, then all you have to do is match up the correct midi instrument to a midi track, set the midi track's midi output channel to match the midi channel for the instrument in Kontakt, add an audio track, and set it to pick up the correct output from the instrument from the Kontakt instance.
All of the above takes only maybe 3-5 minutes at most, and you will get that time down to super quick in no time at all, as you do it more often.
Bob Bone