Site-level preferences are located in TWiki.TWikiPreferences-17jan2012, however this Public.TWikiPreferences-17jan2012 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)
Site Specific Site-wide Preferences
Set WEBLOGOIMG = /twiki/pub/TWiki/physics_logo.png
Set WIKILOGOIMG= /twiki/pub/TWiki/physics_logo.png