Don't try to patch anything until you've identified all that wrong first. Clean out all the rot, THEN being the rebuild... Floor first, walls second, ceiling third.
Thank you everyone for tour helpful advice. We started with the ceiling to see how much damage was done. Turns out there is no rotting in the roof. I believe it was wet from the couple days that it rained here, after the previous owners dad put silicone around the new vents and it did not seal it all the way. That was last week and everything is now dry with no mold.
So the question is do we use the butyl tape and then the Dicor self leveling or the eternabond around vents. And do you use butyl tape with the eternabond tape? And are you supposed to put silicone on the screws before the Dicor or eternabond?