First wave reply...
1.Sound Domain has always been known to be a great place to do business with that offers competitive prices.
2.I would have to agree with the others and say to go with the 2 ohm ID chameleons. You'll be able to get more power to them no matter what amp you decide to go with and the distortion difference between 4 ohm stereo and 2 ohm stereo should not be audible.
4.Yes, chameleons can be purchased as a complete set or broken up into individual componentsand purchased that way.
5.A little variation between what the manfacturer recommends for a sealed enclosure and what you actually decide you are going to use is usually fine. In your case, you're fine. Please!!! Stay away from the particleboard. Stick with the MDF.
6.Underseat amp mounting is an ok thing as long as you have enough clearence for heat dissipation or you have an amp with a built in fan. On a personal note, I have never been a fan of such and I would recommend mounting them on a board to the back of the rear seat. Just my .02 of course.
7.If you're unsure whether you need or don't need a complex hu then don't travel down that path. Keep your source simple and then if down the road you feel you need more processing features...add them on.
Wave two...
1.Hmmmm...choosing the correct amp(s) for the job. Have you ever considered using a five channel amp to power everything? Just some food for thought.
2.As far as the crossovers go, some people mount them within the door, some mount them under the dash and some mount them near their amp(s) to show them off. It's all a matter of personal preference. Me personally, I have never had the urge to show off a passive crossover so I have always tried to keep it as close to the components as possible.
3.Battery for power...preouts for signal
4.if you're going with Dynamat as you brand of choice for sound deadening...I prefer the extreme because it does its job well and more importantly, it's easy to work with. There are tons of places on the net to get deadening material...just look around. Also there are many different kinds as well. All of which work in a similar manner.
5.Dual voice coil= two 4 ohm coils I believe is what you are referring to . 250/500 I believe is referring to the power handling of the subwoofer. 250rms or continuous and 500peak. If you were looking for a refernce point to go by, use the rms wattage when matching amps. Most amps will rate their amps at rms wattage.
6.Good idea on the hu for now...like I said earlier, you can always add it down the road and it doesn't have to necessarily added up front.
7.Bass is omnidirectional it doesn't necessarily fire in a certain direction. So it really doesn't matter on which side you place the sub. When you find out where you'd like to have your enclosure sit you can attach it to the trunk floor with industrial strength velcro if you'd like or eve better yet...before you load the sub, position the box where you'd like it and run a bolt which attaches the sub box to the chassis of the vehicle.

Have I finally caught up with the group?