Hands down the best way I've found is a little adapter that connects to the back of your Jeep stereo where a cd changer would typically go.
About $60 and easy to install. Basically, now I can connect anything with a 1/8" earphone plug directly into my stereo system.
Amazon.com: Precision Interface Electronics CHRY02-AUX Add an auxiliary input to select 2002-04 Chrysler/Dodge/Jeep vehicles: Car Electronics
The link is to the one I bought but make sure you get the one for your model/year.
Is just replace the stereo seriously. A stereo that has an Ipod dock start as low as $80 plus maybe $7 for the wiring kit and whatever a dash install kit runs for your jeep maybe around $20. If your around Ft Wayne I could help you put it in. Its usually really easy.
Will it continue to integrate with the stereo controls on the steering wheel?