Reddit reviews Mythology: The Illustrated Anthology of World Myth and Storytelling

A few pointers:

• Get yourself a copy of Peter Boghossian's A Manual for Creating Atheists and read it yourself. It's a good manual for teaching people how to talk to people of faith about their faith in a non-confrontational way using the socratic method. I liked the audiobook version. Gently challenge him on things he learns at church. Try to get him to explain what he's learned in his own words. Ask him if that makes sense, and so on.
  
• Science: get your kid interested in science, whether it be dinosaurs, astronomy, chemistry, electricity - something. If there's something he's already into, encourage it.
  
• Supplement his church with other mythologies. Take him to a mosque or synagogue. Talk about how different people have different beliefs. Read him Norse and Greek mythology before bedtime. Get him a book like C. Scott Littleton's Anthology of Mythology. It's got lots of pictures.
  
• Cosmos. If you have not seen it with him, you need to see it with him. Prepare to pause each episode when he has a question. Do your best to answer them and if you encounter something you don't know, be honest but follow up afterwards with a visit to wikipedia. You can get it on DVD as well as stream it on Hulu and Netflix, I think. If he likes science shows like that, there are plenty others folks here could recommend.
  
  One common theme here is this: teach him that it's important to value having as many true beliefs as possible. Instruct him on the importance of wanting to have good reasons or evidence for the things we believe. Part of this is the scientific method, but also a general desire for intellectual honesty comes into play here as well.
  
  You might also get some good suggestions are /r/atheistparents.