Before even bothering with zones, I would first get basic 3D playback working. To do this you'll need to use Red October madVR and also configure MC and madVR to playback 3D.
This is all assuming you are using a version of Windows and drivers for your GPU that still support 3D playback. Short of that, you can configure madVR to output SBS or TAB from an MVC encoded MKV, and then - assuming you have a display capable, e.g. a 2016 LG or Sony display, or a projector with 3D support, configure it to display 3D.
There's a lot more to do this - happy to help; not sure your level of familiarity with configuring 3D playback.