Electrical connection sells an Ipod charger/dock connector that hooks into the AUX cable under the front left pocket. I installed mine in the trunk, rank an extension cord up to the aux port. I put the iPod in the pocket of my trunk organizer to protect it and keep it accessible. Got an iPod remote from ABT and velcro'd it to the top of the left handlebar button array where I could get to it without letting go.. Works like a champ.
Or you can just run the iPod directly into the AUX connector. Then you have to worry about setting the volume on the iPod to the right level. Through the dock, it's line level so you don't have to worry about matching up the iPod volume with the bike volume.
Either way you still need to either mount it someplace that you can get to it, or use a remote control.
I've had the Soundgate and J&M CD changer interfaces on my '05, and both units either locked up stupidly often, requiring either the unit to be unplugged and reset, or in the case of the J&M, it would lock up the radio and require the battery to be unplugged to allow it to reset...