When did Ellen and Joe come back from the dead???

They never did... ?

Ellen only reappeared in the episode "My Heart Will Go On" {6x17}, where she and Jo were still alive (temporarily) due to an alternate reality.

And then Jo's ghost was in "Defending Your Life" {7x04}, as one of the witnesses the Egyptian god Osiris called on to judge Dean's guilt.

They're both still very deceased.