PuffinPlot comes with a detailed user manual, provided both in HTML format (for online browsing) and as a PDF file (for convenient printing). The manual is included with the program itself, but you can also read it online here:
For normal desktop use of the program, the user manual is enough. If you want to write scripts that interface with PuffinPlot, or if you want to contribute to the development of PuffinPlot itself, you will find the JavaDoc useful. This documentation provides details of the classes and methods used both by PuffinPlot itself and by scripts that need access to its internal workings. Like the user manual, the JavaDoc is distributed with the program itself, and is also available online.
The ultimate and most detailed documentation is, of course, the source code itself, which is freely available online here.
If you're not able to find the information you need in the documentation, please email me at email@example.com with any questions you have.