You're handing graphviz a list of relationships. Sometimes you know the ideal way to visualize this is a tree, or something with right angles, but graphviz isn't laying it out that neatly. So you create extra nodes, and edges to those nodes, so that graphviz considers it a "balanced" tree or grid. Then you use styling to turn those nodes invisible (showing just the nodes/edges you want). Once I have this correct I usually contain it within a "cluster", and then link that cluster to the larger diagram.
if you want X nodes falling near in the graph you just put them into a box with white lines and they move as one from this point. Can be made with the cluster environment.