For the main speakers, I think it's pretty simple, I use auto EQ for it, or, a laser pointer sitting at the main listening position. But, subwoofers seem a little different, I only know of three little methods of doing it, one being to simply measure from the main seat to the sub, just like the mains, two, let Audyssey set the distances, which I believe takes reflections into account, and only measures exactly the point where the sound hits the mic, or finally, using an SPL metre. Basically adjusting the distances from the main seat up or down till you find the point at which you get the loudest output.
So my question basically is, which is the better option, in terms of getting the best sound at least in that part of setup.