Check it out here.
Basically though, it points out that it's the non-definitive way the show has treated vessels that have led some of us to be very confused as to things like: why does no one seem to care about Adam? Is Castiel making Jimmy cheat on his wife? etc...
I mean, I do hate to point out discontinuity in the show - but...but....Sam being basically an empty but sentient being has really thrown a spanner in the works in terms of knowing how this whole soul business works. I suppose the difference between Sam's sentient body and brain and Ruby's empty vessel of S4 was that Ruby's vessel was brain-dead?
Anyway, all rather confusing, but at least know I know WHY I'm confused.
Because the other day I was thinking about it, and the only other episode that we had Sam's soul someplace else was in Swap Meat (which I hated, btw)...and in that case, Sam couldn't remember what Gary had done with his body when he got back into it (or at least, we assume he couldn't)...and Gary obviously couldn't read Sam's memory when he was in Sam's body... (or Sam read Gary's)....so, that must mean that the soul overwhelms the brain when it is present.
Anyway, interesting fodder for speculation.