B.B.
I guess it would've been easier for you if he was just curious about the birds and the bees!
We are raising our daughter similarly -- me, an atheist and my ex, an agnostic. We've done our best to let her know that there are all different kinds of faith and beliefs; and none are better or worse. This is just what we happen to believe as a family. I stress that she needs to be respectful of other people's religions so she doesn't hurt anyone's feelings.
He may encounter kids who will be cruel to him because he's not Christian. So, just to protect him until he's old enough to be self-assured, you might want to stress how personal beliefs are, and that he should share them with only his closest friends. People can be very hateful towards us non-believers. That's what I always worried about with my daughter when she was little. But she's grown up just fine.
A couple of books that might help -- "Parenting Beyond Belief" by Dale McGowan and "Humanism for Parents, Parenting without Religion" by Sean P. Curley.