In the main menu choose Project → Project Properties.

The settings are split into pages. The tree on the left lists five main pages, each with its own sub-pages; click a page in the tree to open it. Press F1 or click the "?" button in the title bar to open the help for the page that is currently shown.
The settings are saved in the project file. The same window also opens before a disc is muxed with the internal muxer or with tsMuxeR (its title then names the muxer): click OK to start the mux with the current settings, or Cancel to stop it.
Search - finds the settings that contain the entered text. The matching fields are highlighted on all pages, and the tree shows only the pages that have a match (or whose name matches). A main page without a match of its own stays in the tree as the parent of its matching sub-pages, and clicking it opens the first of them. Clear the field to see all the pages again.
Delete all index files - removes the index and info files created by the internal muxer, by the Scenarist MUI Generator or for tsMuxeR (depending on the selected target). These files (*.mes, *.mom, *.ves, *.mui, *.xui, *.idx) are needed to compile the disc. Deleting them is recommended if you have problems with the compilation.
Generate missing index files - generates the index files that are required to compile the disc and do not exist yet.
Run index generation minimized - runs the internal muxer or the Scenarist indexer minimized.
Save as Default - saves the current project settings and uses them as the default for all new projects.