Hi maro:
I'm going to try to to respond to your OP, not sure if I understand exactly what you are getting at. I'm thinking that your question has to do with how atheists think the universe came to be, and be the way it is, if it was not created by God. Is that right?
Of course, I only speak for myself.
First, I don't start from the position of "I know that Allah created the universe, now I'll look around to see how I know that," or anything like that. I try to start from scratch. Here I am, in the world, with the abilities and information that I have; what can I figure out about how it got here.
I hope you will agree that this stance is more likely to result in a correct answer than if you start with the answer and try to justify it.
Further, it seems to me from the get-go that I should try to set aside my childhood religious training, because it doesn't make sense to me that something is true in Peshawar but false in Salt Lake City. God is either God or He isn't, in Mumbai, Tokyo and New Orleans.
I try to start with the minimum assumptions necessary to explore the question, the assumptions that all of us use every day in every other part of our lives, such as the basic rules of logic, the idea that there is a real world out there that exists apart from me, that we share and can talk about, that I can learn about through my senses and the like.
Of course I don't assume that God either exists or doesn't, because that's the question I'm trying to answer.
With me so far?