I've successfully integrated two subs of different makes and capacities into a smooth working system. However, it was not easy. It took A LOT of measuring with REW, MANY different positions and an unconventional final positioning of my two subs (Boston Acoustics PV900 and SVS PB-2000), but I got a very nice response curve. Essentially, the SVS does the heavy lifting below 35 or so HZ, the PV900 eliminates a deep, narrow null around 43HZ and the Anti-mode 8033 tames the strong peak centred on 22HZ. (a good sub EQ is also essential)
The key factor that made it all work, in the end, was placing the weaker sub right next to the main listening position, well away from any walls. Without boundary reinforcement, and a considerably lower volume setting owing to its nearfield placement, the smaller sub does not "try to keep up" with the bigger one. Instead, it acts as a nice supplement to the EQ, which cannot cure a null, and smooths out the overall curve.
All of this would have been much easier with identical subs, I suspect, though with my limited practical placement options (I tried many impractical ones along the way, searching for better sound), it was suggested to me by an SVS rep that, in my specific case, unequal subs might be better. I'm sure he'd have liked me to order a PB-1000 as a supplement (and, one day, I just might) but he seemed quite impressed with what I achieved with the PV900 and the PB-2000. I certainly am.