It really depends on your stereo inputs. Most of the aftermarket radio's have an Aux plug in front of the radio. Some of the newer stock radio's have a Aux plug in front too. This is what you want to plug into your Iphone headphone jack. You just need a stereo cable. If your radio doesn't have an Aux plug in front, then you may look at the radio schematic, and see if it has an Aux plug behind the radio. You do NOT plug into the antenna jack with your Iphone.
FM transmitters are a last option. An Aux plug is the best. There are also cassette adapters which can work a little better than FM transmitters.
Now, to answer your other question, what I did was I routed the Aux plug from behind my radio, through my gooseneck holder. I didn't like the wires hanging in the front of my radio, and getting in the way. I also didn't like putting my phone in the cigarette lighter to charge it. It was creating a mess. I used the Bracketron, and the Arkon gooseneck. It puts my Cell Phone out of the way, it gives me back my cigarette lighter, and removes all the loose wires.