A guy I knew had an F150 with the same problem. What we came up with was making a down firing setup right behind the center console. We put a JL 12 in there and it sounds great. It looked pretty good too. You have to sacrifice seating one person, but I think it was worth it.
There is probably a better solution, but thats what we came up with.
My Ram had little room, I did a JL 8w0 firing down in a center console, it did ALOT for 1 small sub.
Maybe do bucket seats and build a console box, civic seats are always FS on IA.