I think I'm kind of confused by all that. If it helps I have a Maranz 5006 as my receiver.
Ok, let's try it this way. Speakers and subwoofers produce sound waves which is what our ears pick up and translates into sound. These different sound waves are measured as different frequencies. Each driver on a speaker is responsible for different frequencies, but they usually can't reproduce the bass frequencies with enough depth or loudly enough to be satisfying, unless you're paying quite a bit of money, which is why we need subwoofers.
Now the room you place your speakers and subwoofers interacts with these sound waves, especially in the bass region which is why we need things like audyssey or other pieces of equipment to manipulate the frequency response of the speakers and subwoofers to maintain as flat a frequency response as possible (flatter frequency response = more accurate sound). Most commercial room correction offerings are not meant to handle more than one subwoofer, except audyssey subeq and possibly trinnov AFAIK.
Your Marantz has a version of audyssey that is only meant for a single subwoofer, so if you have two, it will do an adequate job of implementing room correction and equalization, but not as well as some of the other things I've mentioned.
Does that help at all?