To use the special features of your MKII, you will first need to load an instance of the Komplete Kontrol plugin. I usually avoid putting channels on the concert level whenever possible, but for K.Kontrol I allow this. As other users have suggested, there are multiple ways to go about this, but here is the method I use:
1. Start by creating a new "instrument" channel strip at the concert level.
2. There is a slot on the newly created instrument strip where you load plugins. You should see all your Native Instruments plugins appear in this list, along with the MainStage plugins as well. Load Komplete Kontrol into this slot. Check out this picture for reference if you are having trouble locating the plugin slot.

3. You're done! Check out the display on your S88 MKII, and you should notice that the "non MIDI" mode has been enabled. You now have full access to the device's features such as arpeggiator and scale modes.
4. Important note: You must run Komplete Kontrol once as a standalone instrument before you attempt to use it in MainStage. When K.Kontrol starts for the first time, it builds a database of all Native Instruments instruments/sounds. If you try to use K.Kontrol in MainStage without first building the database, you may not see all your sounds show up in the browser. You may notice as you install additional Native Instruments plugins that you will have to perform this step again. (Launch K.Kontrol, and let it discover the new sounds before loading MainStage again.)
Hope this helps!