Technically, the system is designed to use one MD per room. That being said, there are workarounds (which are not considered supported configurations). It does depend on a number of factors in your setup, though. If all you are doing is using the core for direct a/v control of the receivers, you are better off getting an ir distribution system from Xantech or the like and sticking with the DirectTV remotes. Are you using MythTV? How is the core connected to the tv's? Are you using a vga or hdmi to component converter and sending the signal through a distribution amp? Do you just have the core connected to one monitor? A diagram of your setup would be very helpful in answering your question.
FYI - a component distribution amp and an ir distribution system would end up costing in the realm of $500. You could build 3 brand new MD's for less than $650 shipped. My point is that if you don't already have the components handy for the former, you may as well get the MD's and have a TON more functionality AND a supported configuration. All you have to do then is pipe the IR from each UIRT's output jack over cat5 down to the machine room. If you would like any specific parts info just let me know.