Luckily most people ignore the manual, but the Civiliopedia entries for BtS, especially on the confusing mechanisms for complex systems like Colonies, Corporations and Espionage, are terse, ambiguous, and woefully inadequate.
Because spies are so easily captured in enemy territory, and because spending espionage points on covert missions reduces your all-important espionage pool, I mainly use espionage defensively. I keep spies in friendly territory for defense (and so I'm constantly having to build new ones), and just stockpile espionage points, for maximum passive benefits and to force maximum cost for enemy espionage attempts. Being able to see nearly everything about your opponents from the comfort of home is a significant advantage, for practically no effort.
Which is probably broken. Collecting information should probably require that you place spies in enemy territory. Like Religions, Vassals and Corporations, the new Espionage system has flashes of brilliance but still feels very unfinished.