Great overview. Auto-calibration systems like Audyssey can optimize your speaker setup given a certain physical arrangement, but they won't tell you the best arrangement. that is where this article comes in.
Here's a quick way to greatly increase the acoustics of your home audio system without going too deep into phase cancellation, etc. While it's not the most technical or even the most exact approach, it's a hell of a lot better than plug 'n play.