Site-level preferences are located in TWiki.TWikiPreferences, however this Main.TWikiPreferences 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)
Reiber Labs Robot Wiki Customizations
Set WIKILOGOIMG = /nxt/pub/Main/WebPreferences/logo.gif
Set WIKILOGOURL = /nxt
Set WIKILOGOALT = Welcome to Reiber Labs Robot Wiki
Set WEBHEADERART = /nxt/pub/TWiki/LegoGraphics/mindstorms0.jpg
Broadcast message for skins supporting a %BROADCASTMESSAGE% at the top of the page: (IMPORTANT: Set to empty message if not used; #Comment out unused messages)
Set BROADCASTMESSAGE = ReiberLabs RobotWiki - Welcome!
#Set BROADCASTMESSAGE = NOTE: Edit and Attach will be disabled today between 05:00 PM and 06:00 PM PDT (00:00 to 01:00 GMT) for a scheduled RobotWiki maintenance.
Set I = <iframe src="
Set FRAME = " width="100%" height=550>
FINALPREFERENCES locks site-level preferences that are not allowed to be overridden by WebPreferences or user preferences: