What happened to the Engwithans isn't spelled out directly, but it is implied in the final exposition after you defeat Thaos that most of them sacrificed themselves to create the gods.
Thaos' origin is fairly clear, he was an Engwithan who received the charge of spreading their new religion and making sure the secret of their creation would never be discovered. If you believe Thaos' words then does have good intentions, he certainly believes that what he is doing is for the benefit of everyone.
How Woedica gives powers to Thaos isn't said directly. But what is said, by Lady Webb among others, is that Woedica "doesn't allow rules to stop her", she "cheats". Meaning that she is willing to directly interfere in mortal lives, something that the other gods have sworn not to do, instead acting through mortal agents.
Eothas is likely dead judging from the comments of others, he certainly stopped communicating with his followers. But that doesn't mean he can't come back necessarily, Abydon was killed at some point by another god and managed to return by creating a new body for himself. Warning, major White March part 2 spoilers:
What happened in Caed Nua is that Od Nua built the dungeon beneath the stronghold, and went mad with grief after his son died so he decided to build a massive adra statue to him. Eventually Od Nua's followers turned on him and he froze himself in adra to prevent his body from being put on display. The adra dragon at the bottom turned up later, and has been feasting on soul energy from the adra statue for ages. The fortress on the surface, Caed Nua, has had a lot of problems because of the adra dragons influence.