Jbpm is meant to be used in Java EE applications. You should be able to use every feature that Jbpm provides in an enterprise application.
Eclipse has no role to play in running Jbpm. You may choose to use Eclipse based graphical designer or you can use some other graphical designer or for that matter no designer just textpad to create Jpdl xmls.
Its good to know that you are developing java in your myeclipse
java which is developed in myeclipseI thought it is developed by a team led by James Gosling some 15-20 years back :). Just as jest.