I think i already know the asnwer to this, But i thought i'd see if anyone else had this problem...
My wife and i each have an empeg and ive got it setup so either or both can be plugged into the home stereo at the same time, right next to eachother. How do you control one but Not the other via the ir remote?!
Having the house completely X-10 compatible im just turning the power off at the outlet for each right now, but id love to have easier way...

You could use an other remote and use Mark Lord Stuff with ir_translate directive in your config.ini

Go to Hijack Site to see what it does ...

You can use a kenwood KCA-R6A remote with one of them, and disable the Kenwood remote control on the other one (option in Emplode).

However this only works in one direction. There is no built-in option to disable the Rio Remote Control.

Some creative fiddling with the Hijack IR translation features might allow you to do what you need, though. Have a mess with it at www.rtr.ca if you're up for some hacking.