Yeah that is the best way to do it if you have Audyssey MultiEQ XT32. That way it will see the stack as a single sub and the near-field as the other sub. Make sure the subs in the stack have the same exact settings, especially with regard to phase. You know, with three subs, you might get a great response without resorting to Audyessey. I can get a very nice response with four subs without EQing of any kind. You might try setting the subs around the room without stacking them, if you have a way of measuring the response. You will have to set distance and phase manually without audyssey though.
If you decide to go with a stack, put something like grip mat between the subs, like
this stuff, so that the subs do not vibrate off each other.