Joe,
Each individual code can be programmed individually to work as IR, RF or work as the system "default". The system default can be set as can each individual code with a good deal of liberty.

The RF settings can be set to have the IR (or RS-232 code eventually) be broadcast from any combination of the IRF-6 ports. That is, you can send it to a specific port, multiple ports or all the ports. Again, this could be different for each code and different for the system default. This is nice in the case of an IR conflict and also for the newer hybrid computer/stereo components which require CPU time to decipher IR (thus I have placed mine on a seperate dedicated port, so as to not require the equipment to slow down to process redundant IR).

As I see it (from a programming standpoint) this would have less to do with how many zones you have or how they are configured, than it would with the type of "feedback" you are looking to include in your system. That is, if you want power or video sensors, they need to be configured slightly different. For example, the programming interface includes options to only send the IR signal if the unit is on. This feedback is useful when attempting to keep all of your remotes sync'd up. So what sync'ing equipment you want to use will likely have more to do with the port configurations on the IRF-6 than the architecture of your theater zones.

Also note, the RS-232 module interface and how it connects is not yet clear to me.

Best, Cliff