For clarification, I don't mean atheism in the sense of, "I don't believe in traditional religions or a higher power." I mean the firmer idea of "everything about the world is explained by science."
There's not some ulterior gotcha to this question, I'm just interested in people's thought processes.
The way the question is phrased, it sounds as if you are making some assumptions prior to the question. I don't think the question can be phrased as it is without assuming a few things, these assumptions appear to be:
1) I am somehow separate from my body or brain, I am my soul. I perceive the world through my body and I (my soul) is acting upon it. I am above and behind my body.
2) Free will is some magical quality of the universe but separate from it that can be truly independent of outside actors, a belief that your thoughts are truly your own regardless of what is going on otherwise.
3) A belief that a true "in the now" knowledge of free will vs. determinism can be made and experienced. There can be a difference known or perceived between doing something because of your "programming" or your free will decisions.
I disagree with all three of these.
I am not above and behind my body, I am my body. I am my thoughts, my actions, my brain chemistry, my responses to outside stimuli.
I am not outside or independent of the world. I am not able to independently look at me thinking separate of me. Anything that happens to me can change me.
There is no way to perceive a difference between things being predetermined or my will being free, so there is no effective difference. We see things in the now as our decisions through free will, and since we can't in real time perceive any difference, there is in effect no difference.