As Don's post has pointed out, it was necessary to change the steps for Atheists to complete them.
As you can see, it was agnostics who rewrote those steps. I have no idea how atheists do it, except possibly to ignore the parts of the program that they don't agree with.
I've noticed some in AA emphasize the steps, others emphasize the importance of the sponsor, and others focus on the value of the meetings. Perhaps atheists who use AA simply find the peer support of the meetings valuable.