yEd does not offer a way to enforce the side an edge connects to when you create a new edge or change/edit an existing edge.
However, some of yEd's layout algorithms will try to arrange your graph in such a way that all edges point in one direction. Most notably, "Layout" -> "Hierarchical" will do this. By default, edges will leave their source nodes at the bottom and enter their target nodes at the top. To change this behavior to have edges leave their source node at the top an enter their target node at the bottom, change setting "Orientation" to "Bottom to Top" on tab "General" in the algorithm's settings.
Additionally, if your graph is a tree, "Layout" -> "Tree" -> "Directed" behaves in a similar way (and also offers a "Orientation" setting to configure edge directions).
