I personally didn't try to teach my kids to be atheist or agnostic. I thought them critical thinking. In fact I told them that I'm probably only right about 60 to 70% of the stuff I believe and it's their job to try to figure out what I got wrong.
When religion comes up, I tell them what people believe and then say what I believe. I told them they will have to figure it out on there own.
My kids are both atheist. One if 19 and one is 12. I'll report back on how this all works out out when the 12 is older. ?
Honestly, I don't care what they believe, as long as they thought about it and was about to use reason.

Please check out Stephen Baxter's book: Evolution. In my view, you may want to give this book to an early teenager. One of the best books I have ever read.

No specific books come to mind, but I would say that my own morality was largely shaped by the heroes of science fiction and fantasy stories. They usually go about the story with either no religion, especially in sci-fi, or only fake religions, as in fantasy. It's very easy to see how one doesn't need to subscribe to a particular religion, or even religion at all, to establish a solid moral framework, when you get to see all of your heroes confronting and overcoming moral quandary is without Jesus.