The foundation for the Apotheverse is laid out in the four core stories. The primary points of divergence from canon (and other fanon) lies in two main points. First, that Celestia and Luna (and many other rulers of races) are in fact gods, and as such operate by different rules and different limitations than mortals. Second is the events of Apotheosis (and Triptych), which change the status of Twilight in more profound way than canon does.

There is a rough Universe Bible available (which I intend to update), but I would suggest reading the stories if you're interested in doing any writing in it.