The HSU MBM-12 is designed for that type of setup and is intended to be a different model than your "true" subwoofer. I never really looked into it though.
http://www.hsuresearch.com/products/mbm-12.html
I was looking for a good receiver that could do Audyssey EQ on 2 subs but the only ones I found were the new NAD receivers. I never confirmed that they could configure both subs independently though. In any event, I went with the cheaper Onkyo TX-SR805.
I currently have 2 drastically different subs in my setup - a Velodyne DD-12 and an old Sunfire True Sub Junior (8" w/ 8" passive radiator). I bought the Velodyne thinking the one "high-end" sub would be best. It's more than enough output for my room and the real-time EQ is great. However I had nulls in all of the locations I tried. I wanted to avoid paying for another DD-12 so I just tried adding my old Sunfire. With both subs, I was able to address the null in the response while keeping the volume on the Sunfire really low. The Sunfire has an infinitely variable phase adjustment so I THINK I was able to get it fairly close to being in phase with the Velodyne (using the EQ output). Then I let the Audyssey in the Onkyo adjust them as 1 subwoofer.
I really don't know how much I'm giving up in terms of sound quality though. My thinking was that keeping the volume as low as possible on the lesser sub would somehow minimize the negative impact but it's possible I'm getting closer to the lowest common denominator in performance. I mean if it's loud enough to get rid of a null it must be able to have an negative impact on the sound quality. In any event, I should probably look into replacing the Sunfire with something better (I'd just prefer to not have to pay for another DD-12).