Read section 6 of cube_bot-readme.txt in your /docs folder. I've never done it myself, but it looks quite straightforward. If no waypoint file exists for a map, the map is flooded with them when it's loaded, but as I understand it they may be close to useless, depending on the layout.
Ignore the bit about monsters (and triggers and teleporters) ;) this file was copied from cube.
Ignore the bit about monsters (and triggers and teleporters) ;) this file was copied from cube.