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Here is how I currently do it with Apple remotes, and I've replaced one of them so far with a RF remote because the IR repeaters that I have suck.
When Remote Buddy recieves commands from the home theatre remote, it turns on the reciever, the projector, and start either the bluray player, or eyetv depending on what button was pressed.
The upstairs remote turns on the distributed audio system and starts music playing.
It all works really well, but if I could get rid of the IR flakiness, it would work even better. I've been playing with the RF remote, and I love it.
Thanks,
Clay