The developer package you download from connect.apple.com is a full JDK in its own right, there's no need to link the sources to the JRE under /System. You just need to let Eclipse know that there's a new JDK in '/Library/Java/JavaVirtualMachines/' and make that the default in your Eclipse execution environment settings for 1.6; all your projects for that environment will pick up the new JDK along with the sources and docs. I link the specific JDK to 'latest' under the JavaVirtualMachines' and use that in Eclipse; that way I can just recreate the symlink after upgrading to a newer JDK and my IDE doesn't have to care.