The most likely solution will be to have the active sub facing a wall or corner of the trunk...much like putting a home speaker in the corner seems to make "more" bass. The next most likely solution will be to mount it directly behind the seat, active sub facing rearward.
I can't see mounting it with the passive, or active, side down unless it has "feet" to keep it up off the mounting surface.
Bottom line will still be the same - taking advantage of a loading surface, wall, floor, etc., usually produces an impression of more bass. In a car it also produces more rattles.