So guys, this one was driving me crazy and I couldn't find any solution.
Gladly I was able to fix it.

The problem:
When using Kontakt 6 (AU) in Ableton I was able to create multiple output channels for several Instruments, but I wasn't able to route them into more than one of Kontakt's "physical Outputs".

The solution:
Close Ableton (or other DAW) and open Kontakt 6 standalone
Make sure to select your Audio Interface in Kontakt settings
Press "+" next to Outputs to add output channels.

Quantity: How much Outs you'll need (+1 if you want to route all instruments (Output 1/2 is master out)

Number: Choose 2 (Stereo), 1 (Mono)
Soundcard: Choose Channel 1 of your Soundcard
Check "Ascending output assignment", "Delete existing channels..", and "Make this your default config.."
Hit ok

You'll now see the output channels you just created (you wont be able route them to several physical outs yet, don't worry!!)

Click "Presets/Batch Configuration" > "Save current Output section state as default for" > "All Formats" (or just AU/VST)
Close standalone

Open DAW again and load your project
Open Kontakt AU/VST in your DAW
Click Presets/Batch Configuration > Reset Output Section
The channels you created in kontakt standalone should be back

Now you should be able to set all those output channels to new created physical outs.

Save your Kontakt multi and your project.

Just repeat the process to add more physical outputs.
Best way to route Kontakt in Ableton is using the "external instrument" plugin.
Change "Midi To" and "Audio From" to Kontakt's Midi In / physical out of your choice.

I hope this will help some of you.

 

Last edited: Apr 11, 2020