well I have tried possibly every single option you mentioned for positioning and then some.. I have a 92 civic sedan and I found the best setup to be a ported enclosure with the woofer facing up and the port pretty much right against the side of the trunk
__________________
| Trunk ____ |
| |SUB| | Port Facing Side Of Trunk
| |___| |
|_________________|
However this is the best setup for having the rear seats not folded and up.. if you wanna drive like a wanker

with your rear seats folded down then I found it doesn't really matter.. The above setup is pretty much the loudest I have found for having the sub closed off from the cabin.