IWill Audyssey be able to set up with the 2nd sub? There is something in the manual that indicates to me that it might, but I was told by someone on here a while back (can't remember the name) that the 2 subs wouldn't be in phase.
My question is if this receiver was designed to utilize dual subs, then why wouldn't they be in phase, and if they wouldn't, is there any point in investing in a 2nd sub?
The subs wouldn't "necessarily" be in phase, depending on where you've got them placed. Commercial subs generally come with at least a 0/180 degree phase switch, and better ones have variable phase dials.
The thing about the SR6005's subwoofer output, is that they're supposedly not discrete. That is, the same signal is sent to both subs, rather than each sub EQ'd independantly.
This means that time delay or independant trim levels are not set. It's basically the equivalent of using a Y-splitter to use two subs. It can still work, but it won't be as optimized as having the right electronics properly isolate and calibrate the subwoofers' individual behaviour. The subs' combined behaviour is calibrated by Audyssey instead, presuming it's not seriously problematic cancelation between the subs.
Multiple subs are still recommended, although eventually you still might want to implement some signal processing in order to integrate the subs as best as you can and play with unconventional placements.