First, there isn't much documentation on the home page. I would strongly suggest going to tutorials.cytoscape.org and going through some of the tutorials there.
Second, as to your specific question: edges don't have a Z-order, so you can't modify the order of an edge. On the other hand, if your network is so dense that you can't track an edge from one node to you other, you may want to consider alternative visualizations or perhaps changing the transparency of that edge in comparison to all of the other edges (i.e. make that edge much more opaque).