Site-level preferences are located in System.DefaultPreferences, however this Main.SitePreferences prefs topic has override priority and should be used for local customisations. This allows for easier upgrades as you don't need to worry about the shipped preferences clobbering yours. It's easier to keep a handle on if you only copy over the settings you actually change.
Quick edit of existing preferences (edit the topic text to set new preferences)
Set WIKITOOLNAME = UMWiki
Set SKIN = umn, pattern
Set PATTERNSKIN_THEME = /pub/Main/SitePreferences/theme_umn.css
Set WIKILOGOIMG = /pub/System/WebTopBarImages/logo_uofm.gif
Set FAVICON = /pub/Main/SitePreferences/favicon.ico