I've done the same with my system. Here's what I did.

I have a denon head, that for sonic reasons wanted it close to my amps in my trunk. I used a Xantech IR "eye" which runs off of 12V. You connect the eye, power and an emitter to a connecting block (CB12 will do) and off you go. The "eye" I used was quite small, aboout 1/2" in diameter. I would recommend using the SUN490 kit for this product that does diminish range (Your in your car for God sake, big deal) but more importantly allows you to operate your remote when it's sunny. Works like a charm!