What size and how many subs to put in my Civic

I have a Civic Coupe and I want to change my system around but I need a little advice. The reason I want to change my system around is so have a little more room in my trunk. I want to put my subs and amp below the trunk floor but I will probably have to lift the floor up around 6 inches or so. Currently I have 2 10's plus 3 amps above the trunk floor but like I said I want to put them below the trunk floor and have a little more room in top.

Currently this is my setup:
Amps:
RF 551S 2x140
RF 351S 2x90
RF 501bd 300W(4ohms) 600W(2ohms)

Speakers
Polk 6x9 MMC690
Polk MM6 components
2 sony 10" subs which I plan to upgrade to Polks (the sonys are really bad)

My music tastes range from rap to alternative in case that matters on the sub question.

So my question is do I try to go with only one polk 10inch sub which would fit in the tire well perfectly and not having to raise the floor to much or should I go with two polk 10inch subs and have to raise the floor a fair amount? How much will I notice in the sound difference between the two? I guess if it is advisable to stick with 2 subs them at that point I could go for two polk 12 inch subs, would that be any better?

Also If I go with 2 subs and still plan for having everything below the trunk floor but raising the floor up lets say around 6 inches (the mounting depth for the subs are about 5 1/2) and make 2 boxes the appropriate volume, would it matter that the sub depth is just about the same depth as the box?

thanks for the help