Do you have the CD player in the trunk? The cable for that has to have left and right signals that could be connected to a miniplug to go into the top of your iPhone. Personally I prefer the miniplug route because you can still control the iPhone directly (radio controls of iPod/iPhone suck.
It is an excellent idea to use the CD changer input. Much better quality than a cassette or FM adapter. I am not familiar with the Fujitsu Ten/Eclipse in the LS but in general, the problem with the CD changer input is that is not activated unless a CD changer is connected. For this reason you need something that will emulate a CD changer. PIE is one company that makes these. Maybe the model you are looking at will work. There are a few other companies out there, including GROM, although they mostly support OEM radios, not aftermarket ones.