I’m really confused about how much of Earth-One’s, Two’s, and New Earth’s history is currently canon to Prime Earth, and what about the histories of Earth’s four, X, S, Vertigo, and Wildstorm, are some of those stories canon too?
Yes and no and maybe.
Some version of stories from all of those universes are part of the current main universe's continuity except Earth-X.
DC has rebooted itself multiple times over the years, so it doesn't really have a strict canon.
DC mythology is as expansive as Greek mythology. Every interpretation of DC is equal in their legitimacy and appeal to a particular audience.
What do you think?