If you are running a stock head unit then you will probably need to get an FM transmitter. There is one designed for the iPod or you can just get a generic one. It basically allows you to tune your radio the FM transmitter frequency to listen to the iPod.
The other way is if you have an aftermarket headunit with a Line-in or Aux-in connection that you can use a 1/4inch stereo cable to hook up your iPod directly. Most aftermarket units don't come with aux-in, though so a FM trasmitter may be your best bet.
For the moment I've only been using the line-out stereo jack on the dock and relying on the battery. I've been meaning to rig up the iPod firewire cable for power so I can charge it in the car, too, but that requires me buying some stuff (a second iPod firewire cable and the cigarette lighter adapter thing). I've been sort on $$ so I haven't done it yet, but I hope to get to it soon.
I figured I can connect the standard firewire end of the cable to the cigarette lighter adapter and then get a spare cigarette lighter (from Pep Boys or whatever) and wire that in to the electric and store it all behind the dash out of sight. That is the plan for now. Comments or improvements welcome.
correct, I assume that your fancy HU has some sort of aux. audio input on the back. I only have experience with Alpine HUs, but the principal is the same for all.
For the Alpine HU's you need the AiNet adapter change the input for the CD changer to standard RCA plugs.