I wanted to route each instrument in a Kontakt instance to a separate channel in Cubase, so that I can process them individually. The goal is to have a single instance of Kontakt with multiple instruments, and be able to control each one as an instrument channel within Cubase. This is not the same as having an Instrument track for each instrument, since this would use a separate instance of Kontakt for each instrument.

In terms of Whole-Play, this means I can set up a generic system to manage various parameters of a Cubase channel, and they will work for instruments in Kontakt or for any other VSTi.

Because this is the typical thing one completely forgets, I document it here for personal reference, and in case it helps other people.

Versions: Kontakt 5.6.5, Cubase Artist 9, OSX 10.11.

Part 1: Cubase

• Add an instance of Kontakt to the VST Instruments rack. Three options here: Kontakt 5 (64 outs), Kontakt 5 16-out, and Kontakt 5 8-out. You'll be asked if you want to create a MIDI track for this plugin, you don't have to.
• In the VSTi rack, click the arrow next to the name and choose Activate Outputs. Here you check which outputs you want in this particular project.

Part 2: Kontakt

• Open the Kontakt UI by clicking the edit button in the VSTi rack.
• Show the Outputs section in Kontakt (that's in the layout button in the toolbar).
• Click the + sign at the top left of the Outputs section. Here you choose:
  • Quantity: how many outputs you want to make available for Cubase.
  • Number of channels: choose 2 if you want stereo channels in Cubase.
  • Soundcard / Host output: choose the first entry (should be Kt. st.1)
  • Ascending output assignment: tick this one.
  • Delete existing channels before creating new ones: tick it too.
  • Make this your default configuration: according to the link at the end of this post, this should be checked, for some naming reason, but I'm not sure it matters.
• Add your Instruments. In each instrument header, choose the desired output.

Reference: https://support.native-instruments.com/hc/en-us/articles/210300745-Routing-KONTAKT-5-to-Multiple-Outputs-in-Cubase