From what i get, the connections are like this:
Billy has a mother, he never knew his real dad (it turns out later it was Juarez)
Billy had a stepfather, called Thomas, who was married with Billy's mother... Thomas has also a brother, that brother is Ray, Thomas doesn't like Billy for some reason... And because of that, his brother (Ray) has got the exact same impressions of Billy, because all he heard about him, is bad stuff
Juarez, is Billy's real father, and he was either married, or a lover of some sort for Billy's mother...
PS
Don't always take Ray's sayings literally... he's speaking stuff that must be understood in other fashions sometimes i think... Metaphors..?

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About the meddallion, billy DID lose it, but when he looked at the graves, he said he could still remember the exact shape etc of it, therefor a ghost pic of it appears when he looks through the stone-cross holes
I suppose that is what you meant when you say he lost it, buit it's still there..?
[edit:]
It's already some time ago i played it... only got through it once... i have too many games to play through

so i might have messed up the facts a bit, since i don't remember everything all that well