What is the best position for the sub?
 

Towards the trunk door right?

Usually that is the best orientation, yes. It is rarely, rarely recommended by audio enthusiasts to have your sub firing forward. Sometimes people like to fire their subs upward, but this is generally for people A: In a hatchback and B: Who want to get rid of rattles (hatchbacks are bad for them). This makes their sub louder, but they lose a bit of sound quality.

For our trunks, backwards firiing is ideal. If you need more sub bass output, I'd recommend sound-deadening your trunk. That will help a ton. I'd also recommend getting rid of your rear speakers because A: The pressurization from the sub in the trunk will cause the speakers to buzz and distort B: Rear fill only creates soundwaves that help cancel out other frequencies you're listening to and C: (this is most important) Having access holes from your trunk into your cabin allows the bass to be louder and cleaner since it doesn't have to work as hard to "push" through your seats.

Guess that's a long way to answer your question... but yes, point your sub towards the back of the trunk. =]

-Jomero

Actually having the subwoofer firing into the cabin is the most ideal, if of course you are willing to seal the cabin off from the trunk to eliminate cancellation.

Otherwise facing backwards works well, just you will get rattles.