The settings window allows you to control album-wide aspects, any changes made here affects the generated album only. Each album project maintains a unique set of settings. These album-wide settings (unlike image specific settings) needs to be saved with the album project to be persisted so remember to issue File->Save project when you're happy with your new settings. The album project settings are by default stored in a file called "jalbum-settings.jap" under the album project folder.
The settings window is divided into the following sections:
At the bottom there are two buttons: "Ok" and "Apply". You usually only use "Ok" to confirm the settings and close the window, but when in Preview mode, these buttons operate like this:
As "Apply" keeps the settings window open, you can easily play around with the settings and almost instantly see the result by just hitting "Apply".
Some skins have their own help pages for settings specific to them, see Skin Manuals for a list of skins with user manuals.