first timer from tennessee

Ok, newbie here. I've been browsing these forums for a few months and am about to start my project on my Scion XB. I think I've got the fiberglassing partly figured out. But what about the wiring? First off I'm wanting to do two 12" JL audio subs with the amp in between them. All recessed in the fiberglass. How do I run the wiring? Do I just make the sub connectors right beside the amp so there is not much wire to be visible? And as far as the power and ground, do I run a tube from the amp's recessed box out the back or bottom, through the box?  Sorry for all the questions, just want to make it as clean as can be. 

Thanks in advance!

What amp are you planning on using?

For your power and ground, whichever you think will look cleaner. Since we do not have pictures or drawings of your plans, we can't make any suggestions.

I also own an xB, with a decent system.  Bellsracer's right, it would be helpfull if you had some sort of sketch of what you want to build.  Describing in detail will give viewers a better idea of what you want the final product to look like.  I understand your concept, but do you want the subs protruding out or sunken into the box?  Will the subs be mounted cone up or magnet up?  Do you want just the aluminum casing of the amp to be visible or do you want to show the terminals and rca jack connections?  The possabilities are endless!  If built a certain way, you might not have to "pipe" wirring to the amp through the enclosure.