I use Kontakt with Sonar 7. There are two ways to go about this: the easy way, and the hard way.
Hard Way: Set up a blank audio channel and blank midi channel. Load Kontakt into the Audio track, and then link up the midi track. The first midi channel will correspond to the first instrument in Kontakt, and so on like that. Be warned: Using this method sucks sometimes because Sonar does this weird thing where it wipes your settings for all your Kontakt plugins. Fail.
Easy Way: I only figured this one out last week, and I'm so happy I did. Start a new project, delete all the default audio and midi tracks. Go to "Insert" and then pick Kontakt from "Soft Synths". It will load a folder, a synth track, and the MIDI track, which will already be linked to Kontakt. It's a one-step process to get going. From there, you can put in new MIDI tracks as you like, corresponding to their slots in the Kontakt player. The great thing about this method is that it automatically saves all your custom settings in the Kontakt player so when you load the project, you're ready to go right away.
So to directly answer your question, each instrument in Kontakt matches up to the corresponding MIDI channel. If you want to have 8 instruments in Kontakt, you'll just need MIDI channels 1-8
If you want to start adding effects and filters, you'll need a new Kontakt player for each track with an effect.