I believe it was poorly explained intentionally, because it makes the religion more realistic as most if not all religions in real life don't give you all the answers, and most answers are decided by people who run organised denominations rather than by the original details of the religion.
But yes, the XIII religion is complicated. The general gist of it is that most people believe the Maker has abandoned Gran Pulse, leaving it to it's own devices. I don't think Etro (the Goddess) is a third level God, though, I believe she was made by Maker. Barthy was designed to be like Satan - a fallen angel (fal'Cie). There's also that Lindzei guy or something like that, but I'm forgetting details now.
I also remember there being some mention of religion in FFVIII. I think it was in or near Zell's mum's house.