Are all kenwood head units using the same remotes or are there different ones (some of which are the same as Empeg)?
As far as I know, Kenwood uses the same IR codes for all its car stereos. Therefore, the Empeg's Kenwood remote will also control your Kenwood head unit.
If I get the Rio remote, then that will control the Empeg without controlling the Kenwood right?
Right. It uses a different set of IR codes.
However, even if I had that Rio remote...the minute I pull out the Kenwood remote is it going to send my Empeg a flailing as well?
Yes, in the current version of the software. But version 2.0 will give you the option to ignore the Kenwood IR commands, which will solve this problem.
My feeling is that right now, you should buy a Rio remote, and simply don't use either of the Kenwood remotes for a while. Just control your Kenwood head unit with its front-panel buttons.
Then, when version 2.0 of the software comes out, you can put your new Kenwood remote back into service controlling your new Kenwood head unit.
___________
Tony Fabris