Due to the extremely long wavelengths, subs interact with entire room in many, it not most setups. A VERY rough rule of thumb is to either have subs against a wall, gaining another 3db of efficiency, or make sure they are more than 10 feet away from the wall. Keep them on the floor and do not put them on a raised stage. If you are setup near a corner, maximum efficiency is normally a corner loaded cluster where the 3rd boundary adds another 3db. Yes, that's a total of 9db, 3 for paired, 3 for the side wall and 3 more for the rear wall. This is not something to be ignored!
On the other side of the coin, in some situations it is better to separate the subs when you have weird room acoustics which create too much bass at certain frequencies or when you are on a stage and the "backwave" of a center cluster in front of you makes you sick. (That would typically be a room you have been in before and had problems.)
Also, not all subs are omnidirectional. Horn loaded subs are somewhat directional and help noticeably when setup in front of you. In fact, with some science you can create a fully aim-able cardioid pattern sub array.
Lastly, when the subs are not stacked under the tops you may want a means of delaying the signal to re-align the frequencies, espcailly if you are corner leading. However, the re-alignment is set at a single point and much like the infamous automated "room eq" processes, while it is "correct" at that single point, the rest of the space is not correct. You really want to set it up to get the best average sound throughout the entire space.