We're still waiting for the manual PDF file to be made available, so I'm theorizing a bit. If you need balanced outputs for the second zone and want to use the independent second zone control, I think you will need to go from the unbalanced second zone outputs (which is a stereo output, no sub) to your distribution system. How that interface works would depend on how you are implementing the house-wide distribution - most that I've seen use a central amp and distribute directly from the rack to the speakers.

The only case I can see that you should need to re-integrate the sub into the left and right channels is if you elected to use the main balanced outputs and distributed to speakers that could reproduce data below the crossover point assigned to those speakers. In general, the in-wall or in-ceiling speakers that I've seen used for whole-house systems like this did not tend to reach down into the realm of 40Hz or 60Hz (or even 80Hz in many cases), and in those cases the subwoofer data would be useless anyway.

Does any of this help you out?