2006 civic EX box help.........

i think the best way is sub and port back, but thats just my experience with trunk set ups.

I have an 03 civic with a trunk and the best spot in my trunk is port/sub facing trunk lid 6-10" away from it.

I have the 02" model which is the same. sub back port back. I've tried everything else and this configuration works best unless you fire into the cabin with the trunk sealed off (very difficult to do though, the rear deck has a ton of holes/gaps to fill in). Get the sub box as far back as you can in the trunk and put sound deadener on the trunk lid so it doesn't rattle