If you are talking about Workspace Preferences->Java->Installed JREs, then in your case there will not be much difference.
Both probably point to a version 1.6 of Java VM shipped by Oracle.
These JREs are not used to compile your code in Eclipse ( at least not directly, they are specified as dependencies in project build path->Libraries tab ). Instead they are used to provide an execution environment when you are running/debugging your application.
They start to come in play if you need to test your code running against JREs shipped by different vendors or against earlier versions of Java.
From my experience with Eclipse, you do not need JDK to compile and run programs.
However, it is a good idea to have JDK installed if you are doing command-line builds.