Hi, I have been fiddling with Kontakt3 for a while as I'm pretty new to Logic, well DAW's full stop let alone Kontakt3! What I ended up doing is creating a instrument channel and loading kontakt3 in a 16 stereo out format. I then created 16 midi instrument channels with NO instrument loaded. In the environment I routed the 16 instrument channels to the 1st instrument channel with kontakt3 loaded. From 1-16 I assigned each channel (not the one with Kontakt loaded) a midi channel from 1-16. Load a instrument in kontakt3 and assign it to channel 1, repeat a few times for channels 2,3,4,5 etc ect. Now you have one instance of Kontakt3 running up to 16 interments/etc that each have their own midi channel in logic. Obviously you can route the midi channels to aux & busses and record the audio signals but the outputs in kontakt3 to be a little confusing at first!
I hope I got the above right and I hope it's of some help!