Generally firing the subwoofer back provides a greater output due to the cabin gain factor and the fact that it effectively turns your trunk into a bandpass enclosure.
Another popular way is to seal your subwoofers off completely from the trunk and direct fire them into the cabin. This does have its drawbacks as one of the guys on the Civic forum lost about 3 decibels on the Termlab in competition, but his SQ increased due to the fact that his trunk, spoiler, license plate, and a rear deck plastic cover don't rattle as bad. Others have told me that they actually picked up a decibel or two by direct firing into the cabin, so your results will vary with regards to output. The most common difference in doing the direct fire versus in the trunk facing back is that the majority of the folks lose some of that ultra low sub bass when they direct fire into the cabin. Depending on the music you listen to this could be a deal breaker or it could be something you are looking for.
As for your setup, you can do just about anything and the sky is the limit. My recommendation would be sub facing back with the port facing back for the ideal setup. If you can't aero port, then slot port your enclosure.
If that doesn't allow you to have enough room for your ports, then sub facing back with your port or ports coming out of the side or sides.
If you direct fire, I suggest your sub and port facing into the cabin with everything completely isolated from the trunk via a baffle board. This is one of those situations where I would highly advise AGAINST running your port through the rear deck.
I have even built setups for myself with the subs facing back and the ports right under the rear deck speaker holes. If you can pull it off, the results are quite awesome, but it is rather difficult to pull off and sound good! It took me THREE enclosures to get it right last time I did it.
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