It would help if you told us what make and model the head unit was.
All of the CD changers I have seen connect with a multi-conductor cable, and do not use RCA.
For many head units you can buy an adapter that connects via that cable, makes the head unit think there is a CD changer there (and full) and then provides RCA inputs.
On the older Clarion units (2003 vintage) it was really simple to make your own adapter. A few dollars worth of parts, a little soldering and you will have a very nice Ipod adapter.