Audyssey XT32 is great but another option out there that always gets overlooked is the Yamaha Aventage line. Not all of them but the 2 top models (RX-A2000/2010 & RX-A3000/3010) DO have actual dual sub outs including dual sub calibration. Not only does YPAO automatically calibrate for dual subs, but you can go in to Manual mode & have COMPLETE control over the Parametric EQ for both sub AND all the INDIVIDUAL speakers!
I own the RX-A2000 & am taking advantage of the EQ. I have recently spent time EQing my system with incredible results.
FYI: The SubEQ has 4 Bands of EQ power, Frequency adjustment & Q adjustment.
If i were to go with an external EQ system, id go with the Beheringer Feedback Destroyer/Dayton mic/free REW software route. For a few hundred bucks you get a very powerful EQ system. There is a bit of a learning curve BUT once you figure out how to measure correctly, the Beheringer & REW work together & apply the EQ on their own.
Remember though that not all situations NEED such a powerful EQ. If you measure & find the best sub location, adjust the settings on the sub to your advantage & apply SOME EQ (such as found in the Yamaha or XT32) you may find that gets you pretty d@mn Flat.
So if i were you, id take an SPL meter, get some measurements of the room response & see just how flat you can get before EQ. Then if your graphs look like a crazy roller coaster THEN youll know what kind of EQ youll need.