To update Cocos2D, download the latest version ( https://s3.amazonaws.com/spritebuilder/cocos2d-iphone-3.0.0.rc.4.zip24 ), unzip the file and rename it to cocos2d-iphone and replace the version in your current project. It's in Source/libs/cocos2d-iphone.
Credits to Vic at the SpriteBuilder forums for this answer.