As an athiest just like Pullman, I have to say that I can see a bit where he's coming from in his portrayal of Christianity in these books. But I think Pullman's doing two different-yet-connected things in the books: he's taking Milton's Paradise Lost and basically turning it upside down, and at the same time he's taking William Blake's religious mythology and using that as an outline for his own pseudo-Christian mythology. By setting the bulk of the story in Lyra's world, a world which is parallel to our own but different in so many ways, a world where the soul is physically manifested (in a way) in the form of daemons, he's able to create a Christianity that is also parallel-but-different to the Christianity of our own world (and Will's world).

I don't know if that makes any sense, though.

But yeah, the Genesis myth is very important to the foundation of Pullman's trilogy, as it ties in with Milton's portrayal of the creation of the world and the Lucifer-vs-God conflic. I almost want to say that Pullman is taking Lucifer's side in the entire conflict, though I know that's not right...

And I think the religion thing will... evolve, let's say, in the third book. As the rest of the plot becomes revealed, it will definitely begin to come together, and maybe a bit more about Pullman's reasons for doing what he does will become clear.

But I definitely hope you enjoy the third book! The second book is, yeah, the typical middle-book-mishmash, throwing together a bunch of different plotlines and trying to bring all of the characters to the point they need to be at, on the brink of the climax of the third novel, so it's definitely a bit confusing at times. But the Amber Spyglass will hopefully resolve all that.