I've been trying to figure out the same exact thing with my Harmony One...

In my case, I have a Denon 3808CI AVR, which supports 3 zones. Each zone is completely independent of the other. Not only can any zone play any input, but each zone's power on/off is completely independent of the others. This allows you to be watching a movie in Zone 1, and then power on Zone 2 and play music there. You can then turn either zone off, without impacting the other. Of course, all of the inputs (DVD, CD, etc) are completely shared.

I was setting up activities like "Watch DVD - Zone 1" and "Listen to Tuner - Zone 2". But this doesn't work: Assume I start watching a DVD in Zone 1. And now assume someone wants to listen to the radio in Zone 2. If you press the "Listen to Tuner - Zone 2" activity, it thinks I've just exited my "Watch DVD" activity and turns off the DVD and powers down the amps in Zone 1. I want the zones to be independent.

Perhaps there is a better way to model this sort of activity? I'm stuck!