The Settings window can be opened via the Windows>>Show Settings menu item (Ctrl+E) in the main AlliGator window.
It is comprised of multiple pages, which can be accessed via the top page selector:
The different pages are described in their respective manual pages.
Note that any value change done in the Settings window immediately takes effect and is reflected in the corresponding AlliGator window control (if there is one). Inversely, any change to a control in the AlliGator window is immediately reflected in the Settings window.
The value of the Settings controls are saved when AlliGator quits, and reloaded when it is restarted.