This is a good time to step in something that I've been thinking about for awhile. Is it such a bad thing to raise your children to be believers in Judaism, without all the "Voodoo Judaism" as my father calls it. You know what I'm talking about...
You don't know what kind of mind your child is going to have until many years after the basic blocks of information have already been set in his/her mind. Are they going to be a critical thinker or not? Maybe you can guide them to be thinkers, but that's difficult if they're not so inclined and you have no guarantee no matter what the circumstances are.
Given that, if your child is not going to examine things meticulously as you do, maybe he just doesn't care about the details, does it matter what background story you paint for his life to ride in? Ok, so you tell him the idea of God is a crock and so on. He never examines that idea, he's an atheist just because you told him you were. Is that unexamined story any more valuable than the unexamined traditional Jewish story?
Skepticism is a _way_ of thinking, not a specific set of things that a person must think.
If you engender skeptical thought in your child, it won't matter what meta-story you tell them because they will examine it themselves on their own accord. If they're not going to be skeptical, I think I'd rather have a faithful Jew as a child than a faithful atheist.
So I propose that it is best to do both. Give your child the full Jewish education so they understand, or have the basic rudimentary knowledge to understand, their people's religious contribution to the world. But also encourage their mind to think about _why_ they believe what they believe and not so much the _what_ of their beliefs.
Offer the Jewish answers to the natural philosophical questions, but don't claim that they are the only answers.
Maybe they will accept Judaism as adults, maybe not, but at least you've given them a real self-determining choice.
And then there's always the possibility they'll be skeptics with a warm fondness for Judaism just like you.