yEd provides an option (File >> Preferences... >> Display >> Paint Nodes over Edges) to do this.
By default, yEd clips an edge at its source and target nodes, but draws it over every other node which overlaps the path of the edge. This helps you to distinguish edges starting or ending at a node from edges which just crosss the node. If you want the edges to be drawn behind all nodes, you can configure yEd to do so by using the above mentioned setting in the Preferences... dialog.
