The evidence on the question of whether they believed in a Supreme Being is very contradictory.
They believed that there were in the beginning no heavenly bodies, air or earth, only water everywhere, over which at first hovered a formless Supreme Being called Pha.
They had no doubt as to a future state, but no definite idea of a supreme being.
Rather he was a theologian who arrived at his theory of the unity of the Supreme Being by criticism of the contemporary mythology.
The exaltation of Humanity into the throne occupied by the Supreme Being under monotheistic systems made all the rest of Comte's construction easy enough.