You can house a 6.5" speaker in the doors of the 01+ Civics, but it's got to be a shallow speaker and you need a mount for it.
I tried to put a set of eD comps in my doors and they're too deep. I need to order some kickpanels for the car real soon.
My rears are a 6.5" or 5.25", not sure, but they're not 6x9s. I have an 03 EX Sedan.