I don't know if there is a perfect way, because I never found it. For awhile I did Sunday school but we talked about all religion. We would compare and learn about the stories of the religions. It bored them to death and I lost interest too.

I ask questions based in morality in a way someone of their age can understand. I do this to get them thinking. Is it ok to hit? Is x ok for boys but not girls? (x the variable, not Methylenedioxymethamphetamine) What makes a lie bad?

While it is important to allow your children to eventually come to their own conclusions with regard to the god question, you also shouldn't be made to feel as if you have to hide it from them that you don't believe. If they ask you why then you can give your reasons, while also trying to explain why other people do believe. If you present your atheism as something you don't want to discuss it might make them think it is an untenable position, ironically enough, and push them toward a religious mindset. I see nothing wrong in saying that I hope my daughter grows up to be non-religious even though I would love her all the same if she decided to adopt a god at some point, and in exposing her to multiple religions she can judge for herself as she often does that none of them make any sense.

When I was raising my children I was still under the clutches of organized religion so yes I did involve them but I did not force them. And I just explained to them that religion or faith or spiritual things were a very private thing and something that only they could decide.
And that their was nothing wrong with exploring all views and ideas and faiths.
Now that I’m raising grandchildren I have somewhat changed my thoughts.
I pretty much tell them how I feel about organized religion and why. And how I came to believe the way I do.
I do try and stray them away from church stuff of any faith.
I just try and keep them away from the Bible beaters of the world as much as possible. I tell them to use their own minds and talk about all aspects of belief systems.
I answer questions as they come up.
I try and not influence them but leave things open for discussion.

I did not allow my children to be heavily exposed to religion until they demonstrated the ability to reasonably converse about the topic with me, then I didn't limit their exposure, but actively discussed the things they were being exposed to with them, helping them form reasonable conclusions about it, showing them how certain teachings didn't match observable reality, asking them about how people might believe it even if it was false, etc.

I also actively told them that I did not believe, and explained the flaws in the arguments for belief.

but I started teaching them logic when they started talking.