First, you will need to pull out the stereo. On the Pilot, the stereo is in the center stack, below the navigation screen. Car Stereo Help has an excellent database of stereo removal instructions (http://www.carstereohelp.com/stereoremoval.htm), with a specific page for the Honda Pilot(http://www.carstereohelp.com/stereoremovalHondaPilot.htm). If you can, just pull the stereo out far enough so you can see its back panel, without unplugging any of the existing wires. There should be either RCA jacks or another type of unused plug for an auxiliary input. You will need a 3-foot cable that fits that plug, with the other end terminating in a 1/8-inch stereo audio plug. Hook the cable up to the stereo, and feed the other end down into the center stack. Find a spot where the cable can be fed through to the car's cabin. Run it under the carpets to the center console, the look for a convenient gap to run it up into the console's storage compartment. Replace the stereo, and your Honda Pilot should be set for any MP3 player.
I have a 2006 Honda Pilot AWD w/ NAV. I wanted to have an AUX input to connect my MP3 player to the car's audio system. There is an "AUX" selection on the panel. but i need to take the jack out. The dealer told me that there is a jack for the AUX, but it is behind the panel, and i needed to take it out, route it under the center console and bring it out in the center console storage compartment. He also advised me to get it done outside cheaper.
Does anyone know how to do that? or if there really is a wired jack behind the dash, or i have to install that also? I have contacted many shops, but they don't know about this.