I have 2 zones and programmed the remotes to work in either zone. To do this I created a master page that allow the user to select a room. Once the room is selected it goes to that room's main page. The only way back to the main page is to select the room icon in the upper right corner (only available from the room's main page).

In my case there aren't shared resources, though some of the equipment is identical (Tivo, HTPC, and receiver)