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)
Image, URL and alternate tooltip text of the logo for this installation: you should change these settings for your site, or they can be overwridden in WebPreferences for individual webs by defining these settings there.