While driving a MapRoute route, after each waypoint you reach you must confirm that you want to continue to the next waypoint (this is a feature of the Google Maps app, MapRoute has no influence on it). Therefore: when creating a route, use as few waypoints as possible. A route with few waypoints also costs fewer credits.
In addition, pay attention to the route options (found in the Route menu). The option Avoid Highways is enabled by default, while Avoid Ferries is disabled. If you want to drive (part of) your route on highways, disable the Avoid Highways option.
Upon reaching a waypoint, the route usually continues to the next waypoint. If you want to stop or pause at a particular point in the route (for example, at a viewpoint or a restaurant), place a waypoint at that position and mark that spot as a pause/stop spot:
You can also mark waypoints as stops in the Waypointlist.