Ok, if you are putting the box in the middle then face the subs toward the floor. Doing so you will have the magnet facing up but that's ok just cover it with pexiglass, it will look good that way. Make a wooden box, cover it with fiberglass and prep it and get the fiberglass ready to paint and then leave the top all open, mount the sub in there and pexiglass over the top where your arm can rest... that way you can have a sweet armrest and paint it the same color as your car if you wan't and then have a sub in it. The speakers need to be in the doors or under the dash. Kicker has sweet covers for their speakers with spike looking things on them and they are silver and would look sweet in your doors.
Two 12" subs will be nice. Get a KX.1 Class D sub amp or KX multi channel Amp with Sub section (this is the amp to power the subs just ask the Kicker guy's when you order and they will tell you a good Amp). Now for the subs... You got three to choose from for Kicker... High end really really expensive competition kind, in between brand that is really good or the less expensive (but not much more expensive) kind. If you go with the most expensive or wan't to then the Solo X 10 or 12" subs are the best. They say that Kickers 12" sub is like a 15 or 18" JL since they are not round like most subs, they are square. Or you can go with Kicker Solo Baric L7 12" subs or the Kicker Comp 12" subs. Oh wait there is also the Solor Baric L5 sub as well that one step down from the L7.

I know that is a lot of stuff I just put down but I wanted to just show you what they have. What you should probably get is the Solo Baric L7 or L5. L5 is a bit cheaper but still really good.
Then for the front go with something like a K Series Component System which is the mid and tweeds all in one. Ok well for the back you have a bunch of different choices there so what your best bet would be is to just go to www.kicker.com or call them and ask for a 04 Cataloge.
Tell them Shawn Fremin sent ya as well! heh
When you ask for the cataloge ask for a price sheet as well and then just pick from there. Basically to know the best ones is by looking at the prices... the more expensive ones are the best, the cheapest aren't but are still really good.
Sorry if this is a lot to read and confusing but I wanted to just show you everything you would need.
If you got anymore questions then let me know.