How did all the water from the great flood get into Earth's atmoshphere and where did it go?

According the Biblical flood account, the water did not all come from the Earth's atmosphere. The Bible states that the "windows of the deep" were opened in order to allow the rain to continue for 40 days and nights. From the Bible, we know that the deep refers to massive amounts of water outside our universe. Those windows have not been re-opened since, hence why we have not seen that great amount of water.