[Zavien Doombringer]

I believe the Federalist Papers may clear up this confusion.
Thomas Jeferson was an advocate for the freedom of religion and wanted to make sure that government would not have any control over man's covictions to worship God, or a deity. He did quote, a separation of church and state should be maintained, only in defence of freedom to worship, not for the government to be Atheistic. Religion plays an important role in our government and with out religion, our laws would be morally corrupt. Our Constitution was based on the premise of a Supreme Godhead that truth and justice will be judged by Him (God).