Even in their madness, the Anu did not easily kill one another. Those who lost in the power struggles and could no longer maintain their position, fled into their own domains and tried not to attract too much attention. The ones in power could not watch everything.
There were initially some backwater parts of the world where those in power, like Ishtar and her Yahweh, did not have a stake. Here, some of the lesser Anu set themselves up as local deities.
Many of the others who were defeated fled, and banded together. They no longer had access to the ship and the great technology, but they still had some. They created bases in the far north and south of the planet, to hide from both the humans and their own kind.