Irv, I would say that most often integration problems between the main speakers and subwoofers are not caused by the fact that the two are not time aligned. For example, if we place a subwoofer between the speakers and then we move it say 2 meter away from the plane of the two speakers, then at the listening position we will have a time delay of approximately 6 milliseconds between the frequencies emitted by the woofer and by the speakers. As far as I know, most experiments show that the brain considers all frequencies detected within a 50 milliseconds window as par of the same direct sound, i.e. it will detect no echo (repetition of the same sound) for such small intervals. Consequently, I would that this is a second order effect.
On the other hand, destructive and constructive interference (which creates bass nulls and/or significantly reinforce some specific frequencies) cause much more significant problems. Since this depends entirely on the room dimensions and position of the speakers and subwoofer(s) in the room, I would say this is by far the most important complication one faces when trying to integrated a subwoofer into a stereo system.
Regarding two subwoofers vs. one subwoofers issue, two subwoofers yield a more even response in the room (i.e. less null or reinforcements). Most often one can get just as good results with only one subwoofer but this requires very careful set up (this is not two say that dialing in two subwoofer is a piece of cake - not by a long shot).