Hi. My system is also for a 1996 Civic, but it's a hatchback.
I'm just getting started with it. I'm mostly confused about power. All the a/v wiring is no problem, but the power issues make me so nervous about damaging some of my hardware.
Anyway, since you were asking where are good locations to put things, I thought I would share where I intend to put ports etc...
I'm planning on putting a 4 port mini usb 2.0 hub in the empty square next to the head unit. I'm also planning to put a set of aux rca jacks and an ac plug in that little removable piece on the back of the center console. I'm planning on putting a slot load dvd drive in the din slot behind the cupholders. Everything else I'm going to mount in the trunk (inverter, xbox, carpc, av selector).
How's your project coming along?