By default, Graphmatica saves your settings automatically on exit in a file called GRAPHMAT.INI in the same directory the program file is in. in the user defaults for the domain "kSoft.Graphmatica". You can view, backup/restore, or edit these defaults using the command-line defaults tool. Whenever you run Graphmatica again they will automatically be restored. You can save your settings manually at any time by selecting the Save Setup Info item in the File menu.
Note that certain settings (most notably, grid range and document fonts) are assumed to be specific to the current graph document, and are not saved as defaults unless you request that in their respective dialog boxes.
The setup file is just a special equation list that is loaded automatically when you start Graphmatica. It follows the exact same format as a normal equation list (described in Editing Equation Lists) except that when you save it Graphmatica leaves out the labels and the equations (the important parts of normal equation lists).
When Graphmatica saves your options, to simplify things it only records those options that are different from its own internal defaults. (See Default Settings for a list of these.) If your settings are close to the defaults, your setup file will be very short.