Most radio's have a remote wire. This is the wire that you use to connect to the amp for powering it. If not then the ignition wire turns the amp on at all times when the car is started, instead of just when the radio is on. The ignition wire is not the best solution, but it is an alternative.I just installed a Pioneer DEH-X6600BT into a 2006 LJ. I ran into the issue so many of you have mentioned above about the factory sub not working after the radio replacement. I've included some notes below for how I identified the factory sub amp wire, in case it might help someone else.
I've had this Jeep since it rolled off the factory floor, so I know that no one has screw dinked around with the dash wiring. The wire colors in the factory radio harness do NOT entirely match what they should be according to the factory service manual, or any of the documentation at Crutchfield's or Pioneers support. There is no blue wire with a white stripe, nor is there a white wire with a blue stripe in my factory harness.
I ended up reverse engineering the wire harness to identify the wires on the factory harness, then match them with the wires on the adapter for the new radio. Half of the harness is for the factory speakers. The other half has to do with power. I plugged in the factory radio, then identified the +12v power wire, the ignition power +12 wire, and ground. On the aftermarket adapter, there was a blue wire, but the Pioneer harness did not have anything to connect to this blue wire. As a test, I connected the factory radio, verified that the factory sub was working. Then snipped the corresponding factory wire that was mated to the unused blue wire in the adapter harness. WHALLA! The radio kept working, but the sub quit. Probably not the best way to do this, but it worked. I tested and verified the voltage of this wire to be +12v when the factory radio was turned on. Once I identified this correct wire, and confirmed that it mated to the blue wire in the aftermarket harness adapter, I knew I had the wire that ran the factory sub amp. I then spliced the wire back together, leaving the factory harness in tact.
Because the Pioneer deck harness did not have a Power Antenna wire, I had to connect the factory amp wire in the adapter harness to the ignition power cable wire in the harness adapter. This way the amp would get power anytime the Pioneer radio had power.
Works great, sounds... about the same as my factory radio (still have factory speakers). BTW... I had to replace the factory radio because I use my Jeep for what it was intended for (evil grin), so the factory radio has seen too many occasions of getting completely soaked!! Since we haven't completely destroyed the LJ, we are actually cleaning up the Jeep and making it a nice Jeep again. We'll still wheel it, but mainly just mild trails and sand dunes.
The power antenna wire is not a good choice at all. Some people had this problem because the amp and sub only worked when the radio sent power to the antenna, and this was only when the FM/AM source was selected. Therefore, they got no power to the amp or sub for the CD or any other source except AM/FM.
Good catch on the sub wire though. I had trouble with identifying the factory wiring too. I just ran all new wires for all my speakers, and identified the radio ground and radio power wires with an electrical tester.