The School is a research facility that is owned by a company called Itex. Early in the series, they scientists seemed to be working on human-animal hybrids, but later they seem to be working more on superhumans and "brains-on-a-stick". The School says that the scientists are making generations of creatures that will supposedly survive the apocalypse.
The School, as revealed in The Angel Experiment and School's Out--Forever, is located somewhere in the southwest, particularly in the California area.
Jeb worked as a scientist at the School before bringing the flock to Colorado, and returned to California two years later. The flock thought that Jeb had died, and had to return to the School two years after that when Angel was kidnapped by Erasers and brought to the lab. It was there that they reattained Angel, and Max discovered her destiny to save the world.