It's going to be difficult, and not ideal if it can be avoided.
First of all, you need to know how to set up a subwoofer correctly in the first place, let alone 2!!!!
For instance, I recently did a 15 year professional custom installer friend of mine a huge favor by re-engineering and calibrating his home theater system for him. Things were so bad, he called me to see if I could help him. He had 2 subwoofers of different brands in his personal home system, that were most definitely "ill-set up". When I went through his system, everything was off (namely 3 mismatched brands of speakers in system!!!, speakers obscured behind furniture/couch!!!, speakers mis-aimed for tonality, frequency response out of whack, crossover settings off, "dead short" in one of his rear channels, volume levles off between channels, EQ settings all way off, overlapping frequencies between subs and mains, and out of phase, including the subwoofer setup and integration with the rest of the system). Needless to say, his system sounded AWEFUL!
In respect to this post, yes, it was a challenge getting both brands of subs to integrate into the system efficiently. Namely however, the possitioning of the subwoofers in relation to the rest of the system and seating possitions, was a challenge. I ended up having to move the subs into a possition where they coupled with the mains in relation to the seating possitions, for proper crossover and phase parameters. When I got to the system, the two subs were placed on opposite sides of the room, causing phase challenges from different seating possitions in the room. You'd get it close in one seat, then the two subs would cancel each other out from another possition-not good.
My experience and knowledge finnaly got things integrated for tight accurate bass, but it wasn't easy. I noticed both subs exhibited diffent bass quality, when switching between them. I think, even from a "noise/distortion cancelation" viewpoint, having two subs that respond and are engineered exactly the same makes things much better potential-wise. I'd recommend matching dual subs, perhaps set up in stereo, depending. Still, yeah, two matching subs better than mis-match, IME.