What kind of app are you creating? Is this a Web Start app or an applet (hence the JNLP file)? Or is it a desktop app?
For applets and Web Start, I've always pointed JNLP files at JAR files via an URL (file or network). You might be able to create a file URL that points inside a JAR, if that's what you're trying to do.
For desktop apps, exporting JOGL apps from Eclipse is a big topic -- I give some details at
http://wadeawalker.wordpress.com/2010/10/24/tutorial-creating-native-binary-executables-for-multi-platform-java-apps-with-opengl-and-eclipse-rcp/.