When I use both speakers, the sound is more dynamic and has more bass. However it is also less clear mostly due to (I believe) the time difference of each soundwave reaching my ear.

When I just use one speaker, I have clarity but no bass and the sound is not as dynamic.

How do I get the best comprimise?

If I perform a whizzerectomy on the bottom speaker, will this help? I have three extras of the same speaker if I screw up.
Could I use a crossover to effectively eliminate the problem? I do have the ability to bi-amp.
What if I turned the bottom speaker so that it is facing the rear wall?
A combination of any of the above suggestions, or should I just use one speaker (no array) and a bi-amped sub?
I want sound that is as uniform across the listening area (at least as good as it can get)
Any advise on how to get the best comprimise before I cut or spend any money is greatly appreciated! Please do not feel obligated to answer any of the questions I've asked, those were just ramblings in my head.