Yes, you add as many zones in MC as you have output devices and set the specific device in Audio Settings for each zone, then when you play something you can link zones together so they play at the same time. They may not be in perfect sync though. There is a timing adjust facility for these situations although there is no guarantee they will stay in sync. Do you need help in finding where to set all this up?
How are you able to output via both sound cards at the moment without having two separate zones? Are you changing the output device in Audio Settings each time?
Yes, AVRs do tend to not be able to output digital sources onto Zone 2.
Another option for you might be a HDMI audio extractor, which will pass through (I assume) the HDMI signal but also provide a simultaneous output via SPDIF and analogue.
I'm not using HDMI for audio but I have a soundcard with SPDIF and 7.1 analogue outputs. I also have a small DAC that takes SPDIF in, passes it through and also outputs analogue audio at the same time, in other words providing the same function as a HDMI audio extractor would. These sort of things probably work better than linking zones because the synch is spot-on and the computer is only doing audio processing and output once. It's sometimes better to distribute the resulting audio for multi-room situations rather than playing the audio twice through different outputs.
When using the 7.1 analogue outputs, I actually only get MC to use 6 of the channels then I duplicate the front L&R to the unused pair in order to provide a simultaneous second stereo output to go to another room.