There are indeed usually multiple ways to accomplish things in Sonar, and life in general, so my vote is to do what works for the person at the controls.
I too sometimes will reuse a Kontakt multi-instrument instance, and just swap out the instruments, but really I most of the time just create a new instance with exactly what I am looking to use, each time.
Setting one of these up is really harder to type up in a post than it is to actually build, particularly once you have done it a handful of times. In steps, you are essentially only doing the following:
1. Insert an instance of Kontakt (I usually pick the dll with the 16 outputs)
2. Load up the desired instruments for that instance
3. Click on the Batch Function in the Output Section that clears out the audio channels and creates a new audio output channel for each loaded instrument. (It does it all for you)
The 3 simple steps above are all you need to do to set up the Kontakt instance. I happen to also take a minute to rename each output channel to something shorter like: Piano, Bass, Violin, Piano. THAT is not required - I just like it for readability.
Once the Kontakt instance is loaded, I do the following handful of steps to get the audio tracks and the midi tracks inserted and configured:
1) Insert 1 stereo or 2 mono audio tracks for each instrument in the Kontakt instance. I usually use a mono Left and Right track for keyboard instruments, as I will usually also have one of the 2 tracks slightly delayed.
2) Set each audio track's Input to the corresponding Output Channel from the loaded instrument from the Kontakt instance.
3) IF using a left and right mono track for a given instrument, set initial panning for left and right.
4) IF any audio track(s) is going to go to a bus other than the master bus, set the Output for the track(s) to whatever bus you want it to go to.
The above are the simple steps for the audio tracks to go to each loaded instrument in the Kontakt instance.
For the midi tracks:
1) Insert a midi track for each loaded instrument in the Kontakt instance.
2) Set Output for each midi track to the corresponding instrument in the Kontakt instance.
3) Set the Midi Output Channel for each midi track to the appropriate midi channel Kontakt automatically assigned when each instrument was loaded into the instance. (Midi Output Channel is found in each midi track, right under the FX Bin.
The steps above are all that are needed to get the midi tracks connected to the loaded instruments in the given Kontakt instance.
Doing the above steps takes VERY little time.
While the above gets the instance created, and all the tracks inserted and routed as needed, I ALSO then will set each instrument's gain to an initial value of around -18 dB. I do this with a combination of playing a few notes for each instrument (the default velocity is 100), and then setting the Gain knob for each audio track. IF needed, I will also go into the Instrument settings (the wrench in the Kontakt instance for each instrument, then the Instrument tab), and remove the check for the box that is labelled something to the effect of Accept Standard CC 7 and CC 11 Volume changes.
Anyway, the above is really not complicated, and once you do it a couple of times you will be a pro at setting a multi-instrument Kontakt instance up, along with the audio and midi track assignments.
Bob Bone