The Waypoints screen shows you information about additional locations related to the currently selected cache. In the title area you can flip between Cache and User waypoints. Cache waypoints are those defined by the cache owner in the cache listing and might include things like Parking, Trailhead, or the visible stages of a multicache.
User waypoints are those created by you. The most common reason for wanting to create one is to enter the Corrected Coordinates of a solved mystery cache or the next stage of a multi when not directly provided by the cache owner. Some COs have placed coordinates in the cache description. You might want to add these as waypoints.