I am Catholic, so yes I believe in God. But no atoms do not have intelligence, it's simply forces of nature, created by God in my opinion and belief, that act. It's pretty simple. Atoms don't look for each other, they do what they are "programmed" to do. It's nature. Like gravity, it's just there. Yes I know gravity is the force of larger objects pulling on smaller on and vice versa, but this force is simply there, it's nature. No matter how hard man tries to understand this, we simply can't because well we've never "seen" it, and I don't mean visually, it's hard to explain. Take this for example: how would you describe colors to a blind person? How would you describe, red, blue, yellow? You can't say, bright dark, shady, etc..because they don't know what it is since they have never experienced it. How would you describe the sense of touch to somebody who has never had feeling their entire life? You simply can't, just like there are things in the world nobody can understand and never will understand.
A good song about this kind of thing is "Speed of Sound" by Coldplay. All of their songs are good, they have meaning.