Your confusion lies in the fact that the Constitution is the supreme Law of the Land, -- above any of the Federal, State, or local government statutes/laws "to the contrary notwithstanding".
[See Art VI]
What that means (the supremacy clause) is that if the fed gov legally passes a law that it is legally entitled to pass, then the states must obey. It DOES NOT mean that the fed gov gets to pass laws that are not covered in the enumeration, such as telling the states that they can't have state supported churches. But what about my questions posed earlier?