OK, so if you are using Project > Add Track > Instrument Track, you are using the easier way, but this one isn’t for the multi-timbral isntruments. Input of this track is MIDI, output is the sound. In this track, you can find MIDI Inserts, MIDI Sends, and Inserts or Sends too. These last two are “audio”. So you can insert any “audio” plug-in. Same, as you can insert it on the exported audio track.
If you are using Device > VST Instruments [F11], insert the VST instrument in to the virtual rack, and create MIDI track, you are using the second way. Then, you can work in multi-timbral way with the instrument. In the instriment window (it depends on the exact instrument), you can set different output of any track. So, you have Outpu 1-2; 3-4; 5-6, etc.
Then, in the VST Instruments rack, you have to click on the icon right from the “e” (box, and right arrow). You will see the list of virtual output of the instruments. By clicking on the output, you will add this in to the Cubase. In the VST Instruments folder, you can find the folder of the instrument (Kontakt 5 for example). In this folder, you can find all these outputs. So, if you click on this output, you will see Inserets, Sends, etc. Same asi audio track.
Is this more clear, now?