That is what I've heard too. Mixing a decently tweaked sub in with one that sounds like crud in your room maye fix some things, but also make others worse. Calibrate each individually. Depending on your subwoofer options, this may be as "simple/limited" as finding a good location in the room (subwoofer crawl) and setting the right gain and then doing the same for the second sub, then splitting and going from there. You ideally want them at least the same distance from the listening area even if they aren't in the same location so that delays are calculated correctly, and then calibrate them as "one."
My Onkyo TX-NR709 has two subwoofers out, but my understanding is that they are nothing more than an "internally split" signal, meaning that I have no independant control over them via the Onkyo. That is more of a limitation of the Audyssey MultEQ XT. You need the Audyssey MultEQ XT32 to be able to control each sub independantly. I know that isn't directly related to the original question, but since others may have difference receivers, it should help with their questions too.
