Design can never be an ultimate explanation for anything. It can only be a proximate explanation. A plane or a car is explained by a designer, but that's because the designer himself, the engineer is explained by natural selection.
Metaphors are fine if they aid understanding, but sometimes they get in the way.
I don't know what to think about magic and fairy tales.
Complex statistically improbable things are by their nature more difficult to explain than simple statistically probable things.
If children understand that beliefs should be substantiated with evidence as opposed to tradition, authority, revelation or faith, they will automatically work out for themselves that they are atheists.