They're not alternate realities because he is actually in one universe, just at different times.
And it's only difficult because you have no context. To understand the current state of the Batman franchise, you need to read (or find summaries/explanations of) all of Grant Morrison's Batman work from the past couple of years, Final Crisis, parts of Infinite Crisis and 52, and some of his Seven Soldiers of Victory books (which provide more clues as to what the Omega Sanction actually is).
Return of Bruce Wayne is not really a good "jumping on" point. If you're interested in reading Batman, you're better off waiting until that story is completed and Grant Morrison starts the next chapter in his work on Batman. That's probably around the beginning of next year.
DC franchises with good "jump on" points are Green Lantern (GL, GL Corps, Emerald Warriors, Brightest Day), Flash (which is just one title right now), Superman (in June, after War of the Supermen, lots of titles), and Wonder Woman (new writer taking over in June, I believe; one title).