: does a 1-2 inch fore/aft difference in seat placement [change anything?]

Dunno!

: How do you determine the best location precisely?

Ah. I listen to the designer of my boat. And he writes:
"The cockpit should be located so the seat back is about 10" behind [the center of bouyancy]."
Since my 'yak (the Cormorant) is symetrical fore/aft the center of bouyancy is easy to find. From glancing at the Pygmy website, I'd guess that the AT was symetrical fore/aft as well and that the same rule would apply.

Hope that helps!
charles