Presenting Schenkerian graphs
Chapter Five of the SchenkerGUIDE handbook contains extensive advice on presenting foreground, middleground and middleground summary graphs. Here you will find some a summary of notational features, some DOs and DON'Ts and some advice on presenting Schenkerian analysis using the Sibelius music publishing package.
Music notation software has made it easier to produce graphs to a professional standard. I use Sibelius for setting my own graphs and this page offers a quick guide to using this package most efficiently. The tips here relate to versions 4 and 5 (very different!). I hope to produce a similar page for Finale at some point (if you use Finale and have any tips that you would like to share, I would be grateful to hear them - email me on email@example.com).
For a guide on presenting Schenkerian analysis using a Linux-based system, take a look at Kris Shaffer's Making Schenker Graphs with GNU Lilypond