How Sub Dimensions Affect Directivity
The dimensions of the radiating area of your subwoofer(s) determine the frequency range of their directivity. It's often said that bass is omnidirectional — however that's only true for wavelengths longer than the height and/or width of your subwoofer or array. The longer the dimension, the lower the frequency at which the array can achieve some directivity.
Half-Space Radiation and the Ground Mirror Effect
The ground is effectively a mirror to bass — this is called half-space radiation. Two side-by-side subs are mirrored by the ground to provide the effective output of a block of 4 subs in full space. The side-by-side subs present a larger dimension to the ground/mirror, and slightly lower frequencies will be constrained and reflected by the ground.
Side-by-Side vs Stacked: The Short Answer
Side-by-side will provide slightly better performance at slightly lower frequencies, and slightly narrower horizontal coverage.
Stacking vertically will provide slightly better performance at slightly higher frequencies, and slightly wider horizontal coverage.
What About 4 Subs?
If you have 4 subs, stacking them in a 2x2 cube will give you the best overall result. Putting them all side-by-side will start to narrow the sound field slightly — it won't seem as loud up close, but it will likely provide slightly deeper response on axis and farther away.
