As far as I know, the goddess who screwed everything up is a third generation god. There is a god above her who is the son of another goddess. In short, the real "God" of the series made a couple lesser gods who made the fal'Cie we see in the gme.

None of this is explained anywhere at all in the main story of XIII. There is only one God, The Maker, and it does jack in the story.