Site-level preferences are located in SitePreferences, however this 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)
FINALPREFERENCESlocks site-level preferences that are not allowed to be overridden by WebPreferences or user preferences:
The overall skin: