In the Preferences of the Eclipse client, you can change the compare editor that you use.  Just select Team -> Jazz Source Control -> External Compare Tools.  You will see a set of pre-configured options for external compare tools, or you can set up some custom comparison tool to use (if your favorite is not in the list).  If you use your own custom compare tool, then take a look at the settings and macro's used for the pre-configured editors, to get an idea of how to set up your own custom editor.