I'm not sure if you can connect the Ipod directly to the stock AMP. Simply because it takes in a high level input (so I hear, I never tried it myself). If you used an after market amp you could rig something like that up.

It's not going to be easy, your best bet is to get an after market head, bypass the amp, and use the AUX in from the head (not all have such a feature, I know Pioneers do).