I found the eclipse.org article the most helpful to get me started.
A good place to get started debugging the code is to set breakpoints on org.eclipse.jdt.core.dom.rewrite.ASTRewrite, particularly the rewriteAST() method, then trigger some refactorings.
Here are a few you might find useful. Are you looking for anything in particular or a general sense of how to process the AST?
http://www.ibm.com/developerworks/opensource/library/os-ast/
http://blog.sahits.ch/?p=228
http://www.vogella.com/articles/EclipseJDT/article.html