The "Startup Directory" is the directory that Cantus will open immidiately after program startup. If the startup directory can not be found, your home directory will be opened. If your home directory can not be found, the filesystem root will be opened.
The "Show filetypes" lets you specify all filetypes that you consider being of interest for you. You can enter glob-style patterns there. For example, to display .ogg files only, enter "*.ogg". To display .ogg and .flac files as well, enter "*.ogg,*.flac".
By activating the "Show hidden files" checkbox you indicate Cantus not to skip files beginning with a dot (".").