Site-level preferences are located in TWiki.TWikiPreferences, however this Main.TWikiPreferences prefs topic has overrride 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.
(Click for form-based editing of existing preferences.)
FINALPREFERENCES locks site-level preferences that are not allowed to be overridden by WebPreferences or user preferences: