Based on everything that we know from BSG canon, the Gods of Kobol are and were sentient beings analogous to the Greek and Roman Gods. They created Man, but evicted their creation from the Paradise of Kobol after baser instincts led to abominable acts such as human sacrifice and arrogance led to Man 'playing God' by creating life in the form of the original Cylons (the 13th Tribe). We know that the 13th Tribe left Kobol about 2,000 years before their own creators were evicted by the Gods of Kobol.
When it comes to the identity of the Cylon God, Caprica shows us that Zoe, Clarice, and others clearly inspired the Colonial Cylons' monotheistic beliefs, but that there was also an external 'higher power' influencing things as well (the entity who sent the 'Head Angels' to Zoe, Caprica Six, and Baltar). This entity was most likely a Kobolian God, but we're never told why this entity was meddling in things or what their motivation for doing so might've been.