Generally to keep loyalty I build border forts first thing when I capture a province, and keep a unit of peasants in all my provinces that do not border any potential enemies (ie. anything that doesn't belong to your faction - never trust your allies.). These peasants do not stand any chance of defending the province against anything but they are a large unit that needs little upkeep so they are good for keeping loyalty. There are in fact only two things now that threaten me, re-emergences and excommunication. To avoid trouble from excommunication, I always train up an assassin to at least 5 stars and use him to kill the Pope every time he excommunicates me. As for re-emergences, well, the assassin can kill those re-emerging "kings" as well.