Subs in the same location or near the same location by being stacked work like a single more powerful sub by combining their output waveforms. Separating the subs has the potential to balance the output more throughout the room if placed correctly, but less maximum output than 2 stacked subs in the main listening position.
Whether the goal is to maximize the combined sub SPL in one main listening spot or balance the sub output across multiple seats is up to the individual.
Stacking the subs has a similar effect as setting them next to each other. They are basically as near to each other as they can be but when they are stacked the frequency is distributed slightly along the height (z axis) of the room as opposed to an x or y axis.
