What had John been taught in "By the Waters of Babylon?"
The answer to this really depends on the point in the story that you are asking about. What John had been taught early in the story is very different than what he had been taught by the end of the story.
Early in the story, John had been taught all of the same things that most of the Hill People had been taught. He also learned a great deal more because he was the son of a priest. He learned religious rituals, medical secrets, and things like how to read. As John tells us early in the story,
I was taught the chants and the spells—l was taught how to stop the running of blood from a wound and many secrets. … I was taught how to read in the old books and how to make the old writings—that was hard and took a long time.
In other words, John was taught all the things that a priest of the Hill People needed to know.
By the end of the story, though, John has changed greatly. He has been to the Place of the Gods. He has been taught that the things his people believed are not really true. He has been taught that the “gods” were really just people. Late in the story, John tells us
I knew then that they had been men, neither gods nor demons. It is a great knowledge, hard to tell and believe.
So, John has been taught different things at different points in the story.