You've raised a good and complicated question. Let's leave the word "created" aside, since if it has its religious meaning, many people won't find it self-evident.
I take the claim that "all men are equal" to be a way of saying what philosophers put this way: "All persons are entitled to equal moral consideration." It's not an empirical claim, since we don't get the answers to broad questions of moral principle by adding up the facts, though as we'll note below, empirical facts can be relevant to applying the principle.
Notice a few things the principle doesn't say. First, it doesn't say what a person is; that's a hard question that we'll set aside. Second, it doesn't say that only persons are entitled to moral consideration. It might be that some animals are. It might even be - on some views - that parts of inanimate nature are too. Third, and perhaps more relevant to your question, it doesn't say that all persons have the same detailed rights. 10-year-olds don't have the right to marry or to enter into contracts. Murderers don't have the right to roam the streets freely. And people with intellectual handicaps may lack some rights as well, though the devil is in the details.
What specific rights a person has depends partly on matters of facts; what abilities a person has might well be relevant; past actions might be relevant; how others have treated him or her may be relevant. The point of the slogan is that in deciding if someone is entitled to certain rights, only the morally relevant considerations be applied, and they should be applied even-handedly. If some characteristic is relevant (intellectual capacity may sometimes be), then it doesn't violate the principle of equal moral consideration to grant people different rights depending on whether they have the characteristic or not. What would violate the principle is to ignore the morally relevant distinctions to someone's advantage or disadvantage.
Maybe the simplest way to put it is this: the principle says that people are entitled not to be treated arbitrarily. But paying attention to relevant distinctions isn't arbitrary and so this idea of moral equality doesn't call for granting everyone the same detailed rights.