In the first season, we don't get an onscreen explanation for how the Cylons ended up monotheistic, but Ron Moore has given some hints in interviews, and it - and the first Cylon war - will be a part of the backstory revealed in the second season, so I hear. The episodes which deal most extensively with Cylon religion (though it's an undercurrent throughout) and the human religion are Flesh and Bone, Hand of the Gods and the second part of the season finale.
smashcj linked to a review of episode 3 which draws some B5 comparisons I don't agree with but has one fascinating suggestion - picking up on the "the children kill/banish their parents" thing, it asks what if the BSG humans are the Vorlons/Shadows and the Cylons the younger races...
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In the first season, we don't get an onscreen explanation for how the Cylons ended up monotheistic, but Ron Moore has given some hints in interviews, and it - and the first Cylon war - will be a part of the backstory revealed in the second season, so I hear. The episodes which deal most extensively with Cylon religion (though it's an undercurrent throughout) and the human religion are Flesh and Bone, Hand of the Gods and the second part of the season finale.
How far are you now?