Well, when you interactively create edges in yEd, by default edges start and end in the center of the respective nodes. Thus the simplest way to create edges that lie on top of each other is by placing them over each other right from the start. yEd's snap lines (fifth button from the right in yEd's tool bar) or its orthogonal edge editing mode (third button from the right in yEd's tool bar) make placing edges on top of each other very easy.
To place existing edges above each other, either select one edge and drag its ports (i.e. the points where the edge connects to its nodes) and bends to the desired location with the mouse or explicitly set the port and bend coordinates in the properties table in yEd's lower right corner. To set port coordinates, select the edge in question and adjust the values for fields "Source Port X", "Source Port Y", "Target Port X", and "Target Port Y". To set bend coordinate, select the bend in question and adjust the values for fields "X" and "Y". Please note that port coordinates are relative to the center of the respective node. (Bend coordinates are absolute, though.)