I've got the CDA-9855r (the older ones that needed the additional box to use iPods) and my iPod lead comes through the back of the glovebox, with my iPod spending it's life in there tucked away.
Even with the glovebox empty you can't see the hole.
I had the CDA-9856R in my last motor, iPod cable hung in the glove box, it would operate through HU but that car had no steering wheel controls(subaru, no toys, adds weight)
Only certain models of iPod would charge themselves from this unit though.
Cables can be found cheapest on e-bay. Manuals can be downloaded from Alpine website for correct cable part number/fitment.