To start over from scratch with a clean grid and the default settings, choose New from the File menu (or the toolbar). Currently, Graphmatica supports only one open graph document at a time, so you may be asked if you want to save your current work first.
The new grid will have the default values (from your graphmat.ini file) for all document-specific properties--graph paper, grid range, fonts for text on the grid, etc., even if you modified these values in your previous work. However, global properties (such as color scheme, fonts for the edit box, printout window, and status bar, and most of the settings in the Options menu) will remain the same unless you have chosen to make those new setting the default. If you want to change the defaults for document properties before you restart the program, you need to Save Setup Info when you have things set up as you like them.