@Lash,
From reading the witness accounts it is clear that the police believed it was Zimmerman calling for help. I don't think they really knew but went by what Zimmerman said and witness assumptions that the guy on the bottom was the one calling for help.
As for Trayvon being on top, I'm sure he was just before he got shot. But nobody seems to have seen what happened before that, although one witness reports seeing two guys "chasing each other" and yelling at each other.
If you get the PDF there's a witness account from what sounds like a young teenager that is very interesting with respect to the interactions with the investigator. That same investigator later recommends charges so I don't think it's indicative of anything other than the difficulty of making sense of the situation and some natural bias toward Zimmerman because they knew him.