To add a waypoint, use the context menu, drag anywhere on the (connector) edge if the edge is connected, or drag a blue handle if the edge is selected. As you move the edge, new waypoints are added automatically.

Alternatively, right click on the edge and select Add Waypoint in the context menu. 

To remove a waypoint, select the edge, drag it back into a position where the waypoint is removed automatically. 

Alternatively, when the edge is selected, right click on one of the waypoints, then select Remove Waypoint in the context menu. 

To remove all waypoints, right click on the edge, then select Clear Waypoints.