You might also want to check out the book Really, Really Big Questions, a kids' book on critical thinking written from the secular humanist perspective:
http://www.amazon.com/Really-Big-Questions-Stephen-Law/dp/0753463091

I'd also recommend going online to find out whether there is a Parenting Beyond Belief or similar group in your area. We've attended events with our local chapter on a few occasions just to let DS6 know that he's not the only kid who doesn't go to Sunday school or believe in the devil. Kids at school told him when he was only 5 that he would go to hell if he didn't believe in god, so you can't start early enough.

We've been reading myths from all over the world to DS6 since he was very young. As a result, he's already capable of thinking critically about the Bible. For example, when we read him the Noah's ark story, he immediately drew connections between that and earlier, similar flood myths from that same part of the world. I would suggest going to the myth and religion section of the library and loading up. Norse myths are especially popular in our house.