I did something like this some years ago, but instead of connecting an ipod, I was connecting a standard car radio: My wife only listens to the radio (and occasional CD), but I only listen to the Empeg, and also use it, in another dock, in my other car.

Take the amp switching line of the Empeg to a 12v reed relay, that relay admits power from the battery through a fuse to either a 2 or 4 (one for each channel) pole relay, connecting the amp outputs of the radio and Empeg to the amp's input. A further relay switches off the radio when the Empeg is in use

Thus when the Empeg is absent the relays are off, connecting the amp outlet of the car radio (or in this case the volume control from the ipod) to the amp inputs.

When you insert, and switch on, the Empeg, its amp output is automatically connected to the amp input.

That's not 100% clear to me, if you're interested, I'll draw a circuit diagram, I think I posted one before, but I cn't locate it!