It will be an obvious difference in volume.
99% of the time you want it against your back seats facing your taillights. You want as much air space in front of the subs as you can get. And bass is non-directional, so it's false to assume that you want them facing the passenger compartment.
Since it's a store-bought box, I recommend you seal all the inside edges with fiberglass resin. You wont believe the difference it makes.