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Yes. Many HA enthusiasts like to have IR zones where IR is only sent to certain rooms or pieces of equipment.
You can easily do this using multiple MCIR-Links which are specifically addressable by the HCS-II.
To make an even more flexible system, you can combine MCIR-Links with hardwire IR network equipment and repeaters to allow you to move IR in just about any way you can imagine.
A future version of the MCIR-Link will have built in connectors for direct connection to hardwire IR networks. Older boards must use IR receivers and transmitters to link into an IR network.
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Home Automation FAQ : 
Why can't I change my MCIR-Link address?