XNEdit can be customized in many different ways. The most important user-settable options are presented in the Preferences menu, including all options that users might need to change during an editing session. Options set in the Default Settings sub-menu of the Preferences menu can be preserved between sessions by selecting Save Defaults, which writes the changes to the preferences file. See the section titled "Preferences" for more details.
User defined commands can be added to XNEdit's Shell, Macro, and window background menus. Dialogs for creating items in these menus can be found under Customize Menus in the Default Settings sub menu of the Preferences menu.
For users who depend on XNEdit every day and want to tune every excruciating detail, there are also X resources for tuning a vast number of such details, down to the color of each individual button. See the section "X Resources" for more information, as well as a list of selected resources.
The most common reason for customizing your X resources for XNEdit, however, is key binding. While limited key binding can be done through Preferences settings (Preferences -> Default Settings -> Customize Menus), you can really only add keys this way, and each key must have a corresponding menu item. Any significant changes to key binding should be made via the Translations resource and menu accelerator resources. The sections titled "Key Binding" and "X Resources" have more information.