I've got a pair of M&K's now. They're stacked in the corner. Which is almost exactly like a setup I've experienced that M&K tuned (and it's a setup which they feel to be one of the best in the country, if not the best).
Granted they ended up with 3 MX-5000's stacked in the front, and 2 MX-700's in the rear. Which is a little bit more sub than I'm running...
Anyway, they started with 5 MX-5000's in the front. But found that the 3 5000's in the front & 2 700's in the rear worked better. And they've reccomended stacking your subs if you've got a pair of them. It certainly makes it easier to level match the 2 subs with each other, then the 2 together with the rest of your speaks. Not to mention there's less of a chance of them cancelling the other out in some manner if they're stacked.
So try stacking your subs. Try it in the front, try it in the rear. Try it wherever you can place them. Just stack 'em while you're trying out placements...