Position them however you want, and I'll wager most here, if any one here, myself included, in a blind test, will not be able to tell which way you faced them. The difference in sound is that close, minute, not really there, that quite possibly only trained ears will detect the subtle differences and be able to tell you how the subs are faced. Bass is omnidirectional, it's shape so big, that the only thing really affected by how the subs are faced is output on a mic, and that's due to how the wave develops, and if you caught in on a peak. I'll take money even trained ears will have a hard time, repeatily, being accurate in how a sub is faced, in car.
Another sad truth, about in car audio. What happens on paper doesn't translate straight into what happens in car. Too many things affect in car performance, from cabin size, to cabin insulation, to location of braces and brackets to how wore down your seats are and if your sun visors are up or down. Not too mention where your seats are adjusted too and if you have those funky beaded seat covers. Yeah, those seat covers can actually add a little to the output of a sound system. You won't hear it, but the mic will.
My advice? Build it for how you want it to look, and how much trunk you want left. You want a certain response? Build the enclosure to suit that ideal, it's the enclosure that's the most important part of the install anyway.
Hoffman's Iron Law says you can two out of three things. Small enclosure, lowend response or high efficiency. You can't have all three. Car audio is a game of compromise.
Here's a good read from a car audio forum I frequent. It's put into terms better then I could do it, and while it doesn't truly answer the question as to which way is the best to face subs, it'll give you a little insight into how this talk about cargo room, sub enclosure size and power all have to give and take in a vehicle.