Go with putting the two in rear close to each other and then treat them as if they are one sub. Plug those into one sub out. The front into another. Audyssey EQ (subEQ) to your hearts content. Attempt first to set the rears at an equal sound level. That way you will get the most even sound from your rear wall-o-subs. IMO, this is ideal, however you could seperate the two rears as you see fit; just recognize Audyssey will see these tow subs as one and your results in EQing may be a bit more strange.
I am actually going to do this same process with an old M&K 15 inch dual sub in the rear corner and what will be two stacked B&W ASW2500's this weekend. If you want I can pm you with my observation, good, bad, or ugly. I have am older M&K to play with and more bass is to me anyway, mo better.