Recently picked up a new boat with the deck in the glove and found what I believe to be the best solution. I wanted to run the Harmon Kardon Drive + Play, but there is just no way with the short cables. I bought a similar unit to the link below from a local car stereo shop. The one I got didn't come with a line driver, but I spent the 30 bucks on one as well which I'd recommend. I was able to wire in the power and ground right under the dash, the RCA's into the Line Driver, and ran a 25 foot RCA around the bow to the head unit. It looks factory with the only thing coming down out of the dash is the 6 ft. power/play cord. The beauty for me is that it utilizes the dock plug versus the headphone to not only play, but keep the ipod charged, and the line driver gives the signal a boost. I just put a small piece of velcro on the dash so I (the driver) can keep it handy to make the musical choices, and mounted a remote to work the head unit volume.
http://peripheralelectronics.com/prodDetail.asp?strProductID=469&strSearch=