To access the preferences of TOra you select the Edit|Preferences menu item, you will then be presented with the following dialog.
In windows preferences are stored in the registry, but in Linux it is stored in a file called .torarc in the users home directory. If this file doesn't exist a file called /etc/torarc is used if it exists.
To the left is a list containing the available option pages you can display.
The rest of the settings are tool specific and covered under corresponding tool in the tools section(see Available tools).
Selecting a page does not discard the changes of another page, and no changes are saved until OK is pressed. You can always discard any changes made by pressing the escape key or the Cancel button.