Site-level preferences are located in TWiki.TWikiPreferences, however this Main.TWikiPreferences prefs topic has override priority and should be used for local customizations. 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)
Site Specific Site-wide Preferences
Set SKIN = ppe, pattern
Set WEBLOGOIMG = /pub/Main/WebPreferences/ppe_logo.png
Set FAVICON = /pub/Main/WebPreferences/ppe_favicon.ico
FINALPREFERENCES locks site-level preferences that are not allowed to be overridden by WebPreferences or user preferences: