If the 06 is like the 05 interior, then this how-to will help. http://www.scoobymods.com/forums/showthread.php?t=5537
I don't know about any factory amps for the standard stereo. I didn't run into any problems installing my Pioneer head unit. Just make sure that you hook up power to the "power antenna" lead from the head unit. The rear window antenna has an amplifier that needs 12 volt power, otherwise the radio reception will be non-existent.
Random fact: I drove to Laramie, WY once from Boulder, CO to pick up lift springs for my 89 Jeep Wrangler.