I'm not sure what the ideal box for a mojo is. I'm sure someone will chime in on that. The amount/size of port(s) you will need depends on the box size and tuning frequency the sub requires. Its not just a cosmetic thing. The bigger around the port is the longer it needs to be in order to keep the same tuning frequency.
It is hard to design a box that takes advantage of your subs and your car on the internet.
Noone can tell you which way to face your box. Different cars behave differently and considering the high rate of variability in boxes and subwoofer design, the only way to see which will work best is to try it.
The only subs I have done in a Civic sedan were a rear facing ported configuration with single drivers. This was chosen by the owner so it was done. I liked them, but w/o trying different positions I would be silly to say that what was done was optimal.
sub back port forward has generally been the loudest setup ive tried in a ported car. Ive heard alot of people say subs up port back, or port forward is loud, but it sounds like shit in a trunked car imo.