What you describe sounds like the way it usually works in Cubasis, maybe I'm missing something?
If you create a track and set the instrument to an inter-app audio app, playing within Cubasis should play that app, and you'll get sound back from it too.
MIDI channels should also work, but that may depend on the apps you use, and make sure you set them to match on both apps.
Check you MIDI settings in the Cubasis preferences/setup screen too, to make sure it's all as you want it.
When Muting a track, it will do what you say (mute audio and stop sending MIDI).