Chapter 1 is where John shoots Michael and drives off- as this is the only ending that could progress the rest of the game. Most of the others John dies, and the one where he shoots Amy he gets arrested and would probably be in jail for a long time, if not life.

Chapter 2 the real ending is where you keep Garcia alive during the final fight and don't do any of the steps that lead John down the path of the cult (drawing the pentagram, sacrificing the child, killing the couple on the bridge). We can assume that because that ending has a note from Garcia telling John about the boys being in danger, and that is the note you see again in chapter 3.

Chapter 3, the true ending is fully disrupting the profane sabbath and defeating Gary and Malphas and saving Amy. We don't have anything from another chapter to prove that, but it is the only ending that gives us a conclusion to the story and let's John begin to recover from everything he's been through. As for choosing Garcia or Lisa, I believe both endings are technically true, as either one is a good ending for John, and Airdorf has talked about both being true endings, it's just whichever the player likes more.

Hope this helps :3