Huh, two different endings? How does that work, something similar to the Zelda timeline? =P
Well the first book ends, and then the book after that follows one character 3000 years later.
The other series of books begins with a parallel book to Ender's game, but focuses on different characters. Then the following books in that storyline continue in the present.
Ender's Game is the main book, and I guess it's almost like a side series, except that both tie into each other in many ways. They're really good books, though, so I'd recommend them.