The connect method of uavDubinsConnection can accept pairs of start and goal poses. Assume your waypoints are defined as a Nx4 matrix. Each row is one waypoint in [x, y, z, course angle] format. The following two lines should provide N-1 dubin's path connecting all your waypoints.
connector = uavDubinsConnection;
connector.connect(waypoints(1:end-1, :), waypoints(2:end, :))