I like the latest plan with the open theater area. It bothers me that there isn't a sweet spot chair, though.
Since you already use JRemote, I would just setup zones in JRiver. You can easily switch zones in JRemote. Do you want mono or stereo zones? You can control the zones with any iOS, Android, or Windows devices. If you wanted to, you could mount permanent touch panels in some zones for control.
You can add audio devices to your HTPC if you want to hardwire each zone. The new 8 channel Behringer Firepower FCA1616 is only $250. You can also keep the amp in your rack. Then all you need to run is speaker cable for each zones. There are other options such DLNA devices or Airplay that will work with JRiver. You could start with hardwired zones and add wireless zones later.
I recently tested a Solid State Logic Alpha Link DAC for dlbeck's theater (he ended up buying one). It has 16 channels and you can add another 16 channels. You can use any leftover channels from your theater for audio zones throughout your house. You can expand to 32 channels at 96 kHz or 64 channels at 48 kHz.