Ted,

Nothing complex. Perhaps "prime number" is a bit of a misnomer, but not too much so.

I simply situate the subs in positions where they are not at exact multiples of some room dimension. So if I had a room that was 12 feet wide, I would not place two subs exactly 4 feet apart (and four feet from each side wall) if I were placing them along the front wall. I'd instead place them at 2 (a prime number) feet apart, 5 (another prime number) feet from each side wall (as an example). You're basically trying to break it up so that they are not going to easily set up a bunch of standing waves. I'm no physics expert, but this approach seems to have worked well for me.

Of course we can't all start with a fresh sheet when laying things out, so just do the best you can - and avoid some really obvious dimensional matches.

Hope this helps.