Mainly the same places theists do: from their experiences, from their upbringing, from their friends and family, from personal reflection and from the wisdom of those who came before.
There is an enormous range of study going back to ancient times concerning this subject: philosophy and ethics. Different people may have different traditions they find relevant; I lean towards Kant, the existentialists, the good ole ancient Greeks, that sort of thing. But I had some academic training in this regard. I also find that the great literature has influenced me a lot in my view of the world, writers like Tolstoy and Shakespeare explain the human condition for me far better than any religious text. "The Plague" by Albert Camus has gone farther for me in explaining morality in a meaningless world than anything else I've read - it's about a doctor who fights an unstoppable plague. Despite the fact that he can neither save his patients nor prevent future deaths, he struggles on to help them, for we all must do the best we can for each other. (That's an enormous simplification, but the basic idea)
Religions define morality in a set of inflexible rules left over from an ancient time, enforced by a punishment and reward system. A non-theist tends to believe that there will be neither punishment nor reward beyond what we enforce in this life, and that we should do right by one another regardless. Not because we want to "go to heaven", but because if everyone behaved in this way it would be to the benefit of all. Anyone who needs a rigorous system for this should look up Kant's categorical imperative, which works out the same thing in a logical and structured way.
Incidentally, certain religious philosophers, like Buddha and Jesus, said some good things in this regard, but a non-theist will interpret their teachings a bit differently. For example, whenever Jesus talked about the kingdom of heaven being at hand, I don't take it to refer to any "end of the world". To many people it means that if we were all a bit kinder to each other, here on earth would be a kind of heaven. Which is pretty wise when you think about it. So some religious figures and people with religious beliefs can be a source of wisdom for an atheist just like any other human being, but as they are human beings their words are up for interpretation and modification. I had a religious upbringing, but I never could consider "because god said so" to be a good enough reason for anything. If you can demonstrate for me, though, how a behavior benefits my fellow man, I will be glad to use it to guide my decision-making regardless of where that piece of wisdom came from.
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