But then the very next time you make changes to your database and re-generate the graph, you'll be back where you started.
The only true viable option you have is to find some command-line parameters to 'dot' to alter the behaviour of the layout engine, or else to find a settings in the .gv file to tweak which makes 'dot' layout the graph differently.
What exactly are you trying to do?
One option you could try is to produce your Graphviz charts in SVG format and
use an SVG editor such as Inkscape to tweak them.