i've seen these for different types of cars, but i have a 99 accord v-6 coupe, and i was wondering if anyone knew of any of those enclosures that fit in the trunk in the sides, or all flush with everything, that look build in?

Yea they make those "built in look" enclosures. Check in the Crutchfield magazine if you get it. if you dont then just go to the crutchfield website and order a magazine, i believe they are free. :)