I was corrected by a prius owner when I said that it looked more diffiicult to install an afetermarket radio in a prius. Apparantly the prius comes with a spot that you can use to add an after market radio.
As far as subs in a civic. Yeah the trunk space is a pain to work with. So many nooks can cranies. I currently have 2 1.6cf boxes in my trunk and I have some space left over. However, I am looking to redesign my boxes to recover even more space. I also have 3 amps in my trunk one of them being 30"x10" by 3" or so.
If your subs only take up like .9 cubes you can probably build a couple of boxes 12x15x12 and fit them in the sides and not use up much of your trunk. I don't know the actual size your boxes have to be so you can take it from there.
Hot_Georga:
I hear that replacing either the headunit or the speakers will make a difference. Probably not a huge difference but the stock radio in the HCH is so poor to start that anything would help. A full range speaker would do wonders. Add a small amp into the mix and you should be good to go.
BTW: did anyone ever price our speakers from honda? I think the dealer charges $9 for them

that should speak volumes about the audio system in the HCH.