The bestiary is for monsters. (Specifically original monsters that you wrote, not existing things like skeletons/ghosts/wolves/etc. Those you can just say "stats as [monster name]" for in the room or hex key.) The folks living in the towns are npcs, so put the details for them with the town.
The idea with the encounters list was to have at least 20 different things you can run into across the whole hexmap while you're doing overland travel. If you want to write more than that, go ahead. Dungeons should have their own lists of things in them that you make when you write them and the list size for those can be whatever you decide.