hmm.. are they really that picky..they sound friggin awesome, just wish it was in phase.
O_o
Why aren't your speakers in phase? That would cause it to sound like shit. Having speakers in phase is when you have all the + and - connected correctly, so when the speaker kicks out, they ALL kick out. When it moves in, they ALL move in. If they are opposing each other, they cancel each other out... which generally tends to sound like poo and produce poor bass.
Your sub should be set to (depending on a few different things) about 80Hz normally, maybe a bit below. In-car speakers to about 80-100 Hz. Remember even though you set the crossover at 80hz LPF, it won't usually drop straight off there, it tails off. So if your in-car speakers are set at 100Hz hpf, the two signals should crossover in the middle to some degree.
Check your boxes for leaks. Lightly push in the cone of the speaker and see if you can hear any 'wooshing' coming from anywhere on the box (usually occurs around the terminal peice or the speaker itself). The cone should be difficult to push in and when you release it, slow to come back out. I'd also recommend putting SOME sort of padding in the box. If the box is just the right size, only put a small amount in there but try and strech it out over as much of the wood surface as possible inside the box. Both of these (if they apply) should give a deeper and richer bass sound and turn something that sounds like a BANG BANG to a nice BOOM BOOM.
Any of these may or may not be attributing to what you're saying, but they are all worth checking and trying. For box padding/fill I've just been using some craft filling (or something like that) that I picked up from the good sammy's! The denser the material, the less you need to put in and the more it'll strech out.
One other thing to try is the orientation of your subs. Usually the best sounding is facing the subs towards the rear of the car.