^ That's exactly what you should do, have a separate instance of Kontakt on each track.

Since most of the memory used by Kontakt would be taken up by the samples rather than the plugin itself, I wouldn't expect two instances of Kontakt, with one sample set loaded in each one, to use much more system resources than one instance of Kontakt with two sets of samples (though I haven't used Kontakt in a while so might be mistaken).

If you don't want to have to worry about which MIDI channel each track is on, you can select "Forced MIDI Channel = 1" in the second drop-down menu in the Plugins window, that'll force any notes on that track to channel 1 before they reach the plugin, then just select the sound you want on the first slot in Kontakt, which uses MIDI channel 1.

That "Forced MIDI Channel" option is handy, as it saves you from having to remember the channels, or refer to Options - Preferences - Channels to figure out which slot to use.

Cheers
Kent
PG Music