The Preferences option may be opened either with the Prefs button or with the shortcut . Preferences contains configurations to be applied to all scans globally.
File Locations shows the path to temporary files. These files should be located on a separate partition with plenty of free space and without too much fragmentation. If the partition is badly fragmented, scanning slows down. If possible, the temporary files and the scan files should reside on a different partition from the operating system, preferably on a different hard disk.
The menu item Single Scan contains the settings Autofocus, Auto Exposure for ...