as I remember in Company of Heroes cover points are auto placed around obstacles (it uses a tile and area system for pathfinding similarly to my RTS pathfinder), which requires some kind of map decomposition, and they are set as real cover points for each group of characters based on line of sight calculation from enemies within range. thus you can easily assign cover points. if you do not have any kind of map decomposition then you have to place cover points manually, and evaluate similarly in game.