There is a way you can wire the sub and new amp to the headunit. You would probably need to take out the NAV and plug in a few wires but it's usually not an expensive job at a car audio shop. I also recommend going with a single twelve inch Alpine Type R or Rockford Fosgate P3 sub with that Alpine amp. The subs are affordable and you can get a ported box for the sub made pretty cheap. The sub will be loud enough to hear just fine in the cabin.
You're welcome! Usually subs have their own amp but there are multichannel amps that can power for speakers and a sub. The problem with the LS is that it's hard for bass to pass through from the trunk into the cabin. The Alpine you mentioned is the eight inch one right? If so it may not need quite as much power as the ten or twelve inch Type R's.
If you use it on your factory amp it would probably kill it. I would highly recommend a separate amp for the new sub. You can keep the factory speakers and the speaker amp while having the aftermarket sub/amp at the same time. It's what I did on my SC300. The ML sound system isn't that good in my opinion so I'm changing everything out on my car, but that's only because I got some speakers really cheap.
Thanks for the posts on the alpine sub and amp in classifieds. So does the 04 ML have a factory amp for the sub in the rear deck that always blows, do all subs have their own amp? I am thinking I just want to get away from the Lexus sub but noone has a 12 ohm sub? So if I go with the one in classifieds the 300 as listed will I fry my ML stereo amp? If I go with the 500 as you are talking will I have less chance frying my stereo amp and better sound but the 300 would be ok?
If I really want to do this right should I get new speakers foor the doors also? I guess I do not want to change my stereo amp, would that entail taking out the nava and ML system or it is something which connects to it and the nav stays?. Thanks so much I am on the Clubtouareg site and the folks are no where near as classy as our group?