The Infrared receiver built into modern Macs, is only capable of receiving codes from the Apple Remotes. It can not be used instead of a distinct IR receiver. Please note that iRed's Apple Remote triggers will only work with the built in Apple IR receiver.
Please see the PDF The Magic of Apple Remote's IDs for some technical info on the Apple Remote.
More documentation is expected ... on how to use Front Row with iRed2 enabled, e.g.