After this week's episode, I'm further confused as to the identity of Zoom. Despite Eddie sharing Zoom's identity from the comics, Wells still seems like the most likely culprit.
-We already know Wells at least has knowledge of the future, though we do not know if he is actually from it.
-We know Wells is lying to everyone on the show (he does not need the chair), so there is really no reason to believe that the story about his wife is true. Even if it is, it does not mean that that is the reason he is here, especially considering his attention/actions all seem focused around Barry.
-In the most recent episode (6: The Flash is Born), we see Zoom steal the evidence of Barry's mom's case from Joe and threaten Iris's life if Joe continues to dig into it. Joe has been investigating the case in secret, revealing that fact only to Barry and Wells. Eddie is (to our knowledge) ignorant of the investigation. Is it a coincidence that, in the same episode that Wells learns of Joe's investigation, Zoom shows up to halt it?
All of that having been said, I think it would be damn silly of them to have a character sharing the identity of Zoom from the comics, and not have him become him. With that in mind, I have a couple theories as to who is who, and why Zoom showed up in the same episode that Wells finds out about Joe West's renewed investigation:
1. Eddie and Wells are actually working together. Wells is genuinely concerned with the survival of Barry because Eddie (who is actually Zoom and is constructing an elaborate ruse to mess with Barry) has promised Wells that he will change the past and bring back his wife if Wells complies with the ruse and fosters Barry's abilities. This scenario provides a motive for Wells's investment in Barry's survival, while also allowing for Eddie to be Zoom, as his name would imply.
2. Wells is a non-canon Reverse-Flash, and has traveled back in time for reasons that have yet to be revealed, but somewhere down the line Eddie gets burned by Barry (becomes friends, Barry betrays friendship by ending up with Iris, or something) and seeks to become the Reverse Flash.
I'm just throwing things against the wall to see what sticks, but I think those are two possibilities.