Using the factory radio's CD changer inputs should be easy: Just buy an adapter from Crutchfield or a similar stereo shop. It's my belief that such adapters exist for all factory CD changer inputs.
However, there is no way to control the Empeg as if it were a CD changer. You can trick the radio into thinking a changer is attached, but that only lets the line-inputs work. So, as you already surmised, the Empeg will only respond to the IR commands. You'd need an IR repeater if you mounted the Empeg in the trunk.
However, may I suggest that the Empeg isn't designed to be mounted in the trunk and it would be a frustrating experience to use it without seeing the front panel. There are many things it does which depend on you being able to glance at the display. A simple thing like toggling shuffle-play would be frustrating unless you could see the screen telling you whether it had just been toggled off or on.
If your car doesn't have a second DIN space in the dashboard, then I really see only two options for you:
1) Replace the factory radio with the Empeg. Trust me, you won't miss your CD player. And as far as AM/FM tuning is concerned, well, I've got a tuner in my Mark1 and I haven't listened to it for months. Don't need to- I never get bored of my music collection.
2) Buy a different MP3 player that's
designed to go in the trunk and be remotely controlled.
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Tony Fabris