Instead of using the default JRE for running and debugging all Java Application launch configurations, you can specifically assign a JRE for launching an individual configuration.
Launch Configuration Dialog, select the JRE tab.
Note: Changing the JRE used for running does not affect the way Java source is compiled. You can adjust the build path to compile against custom libraries.

Assigning the default JRE for the workbench
Running and debugging
Working with JREs