Tweeter placed under the woofer often puts it farther from the ear than when it's in the "on top" placement, to make up for the fact that the woofer's acoustic center lies farther away- down near the voice coil-cone junction. Placing the woofer on top though, can lead to more diffraction problems from the proximity to another cabinet edge. Either way, IMO the crossover circuit is the key to good sound, assuming decent drivers and cabinetry.
Best,
Roy Johnson
Geen Mountain Audio