
Hmm can't see a reason the box for iPod connection would be way back in the trunk. Most after market boxes (MediaBridge, GROM Audio or iSimple) for external input hook up to back of the head unit via a "Y" type cable.
It is easy, just pull away the front panel, gently, it's held by a few clips and then there is a ribbon cable that needs to be unplugged to completely set it aside, with that out of the way you will see the entire radio, you might be able to follow the iPod cable and unplug it without removing the radio, however if the XM/Sirius cable got tucked away behind it, then you might have to.
Here is a diagram:
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