Kontakt (and all SONAR vst instruments) only has 16 MIDI channels for input. In stand-alone mode Kontakt has more MIDI ports (each with 16 channels) but as a VST there is only one input port. So you are limited to 16 MIDI channels for control. While you can setup 32/64 outputs in Kontakt, you can only have 16 unique inputs. Some Kontatkt instruments (for example complex drum kits) may have multiple outputs but still be one instrument/use one MIDI channel. As a result of this, it is isn't useful to load dozens of instruments into one instance of Kontakt. The only advantage is when more than one instrument all share the same samples. If the instruments don't share the exact same samples the advantages are almost zero.
With the most recent SONAR the easiest way to setup Kontakt involves not changing the names of the 3 Kontakt plugins in the plugin-manager but rather renaming them inside SONAR's instrument browser (with it set to Sort by Category). Renaming it there will stay with the plugin through new releases of Kontakt and will survive a plugin re-scan (both of which will cause name changes made in the plugin manager to be reset/lost). The other option of using the INI file option for VSTPluginNameOption has other side effects on name change. I can't remember exactly what it was, something about changing the names of all the plugins to things that I felt were worse, I only remember hating it, but it might also work for you.
Inside Kontakt it's best to setup the output channels so you can easily assign an instrument to the correct outputs. Then in SONAR when you create an audio track and choose a Kontakt audio output, it's easy to assign that output to the instrument. To do this, inside Kontakt show the Output mixer panel. At the top is a button/drop down labeled "Presets / Batch Configuration". Setup a number of extra output channels by hitting the + (plus sign) in the Outputs pannel. I have 6 outputs called SND1 through SND6. Setup to output as 1|2, 3|4, 5|6, 7|8, 9|10. Then save that as a preset and make it the default for VST Plugin (and maybe defaults for VST Plugin (8 Out) and VST Plugin (16 Out)). I'd do this inside SONAR since in stand alone mode Kontakt has limits on outputs based on the hardware driver you pick. Unless your sound card has tons of outputs you may not be able to setup everything like you can when it's a VST plugin.
Then all you have to do is pick SND1-6 in the instrument (those names show up in the output drop down inside Kontakt) to quickly setup the output. I have a SONAR template with audio tracks with the correct Kontakt audio outs routed to them and MIDI tracks with channels 1-6. This way I can easily load up 6 instruments with 6 separate output. You could do 8 of course (or more), but I didn't bother setting up things I'd never need. That whole rigging (audio channels in SONAR and Kontakt with the pre-defined output channels with friendly names) I have saved as a Track Template. So not only can I use the full Project template, I can also insert it as a track template.
Here's what my Kontakt looks like, notice the sound channels already setup and in use by the instrument:
