It's only confusing if you cling to preconceptions based on the old continuity. Just treat it as you would one of the various adaptations that starts in media res, like the YOUNG JUSTICE or THE BRAVE AND THE BOLD cartoons, and it should work out fine. For example, in the Joker's first appearance in BATMAN THE ANIMATED SERIES, he and Batman already know each other. There's clearly already a history there.

But what is that history? Is it like the one in the comics? How closely does it match? The answer to those questions is, "It doesn't matter. You don't need to know those details to enjoy the present day stories." Same with the history of the new DCU.