Sorry for the thread necromancy, but I was really struck by the secret war concept. I love it.
Also, I would recommend reading a little about the history of Hernan Cortes' conquest of the Aztec empire. There, a tiny group of Spanish soldiers with a massive technological advantage were able to conquer the Aztecs. They manipulated rivals, encouraged/exploited superstitions about the Spanish being gods, etc. in order to accomplish a task that would have been impossible by brute force alone. I think you could easily adapt some of this history to give the alien invaders a rational plan for global conquest.
