Robbie,
I gave this issue some thought as I began to use two subs in my asymetrical room. As an aside, the two subs I use now are two slightly different animals (an Hsu STF-3 and an Hsu VTF-3). There are many complications to your question and without giving us the specifics of your room, sub types, treatment locations, positioning limitations, etc., replies are all speculative.
However, if it helps you, what I did was place the subs in the most desirable (Missus says!
) locations, level match the subs
at the main listening position, and using both subs 'on', run automatic parametric eq with the Yamaha AVR. Then using an AVIA disc, I repeatedly swept the spl's from 20-80 Hz while hand tuning the (continuous) phase controls of the subs until I achieved a reasonably flat FR across that frequency field. I then re-ran the YPAO, double-checked the FR field, and presto....flat response from two integrated subs
at the main listening position. (I don't care what it does anywhere else in the room.)
I hope this helps. It may not be scientifically perfect methodology, but it sure worked for me.