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 SKIN = foswikisite,pattern
Global skin styles. To change the look of the site, point these variables to custom CSS attachments.
Set FOSWIKI_LAYOUT_URL = /pub/System/FoswikiSiteSkin/layout.css
Set FOSWIKI_STYLE_URL = /pub/System/FoswikiSiteSkin/style.css
Set FOSWIKI_COLORS_URL = /pub/System/FoswikiSiteSkin/colors.css
Overriding styles that add upon the global and theme styles. Enabled by default but empty to prevent browsers from fetching %USERLAYOUTURL%-style URLs.