I extract 3rd party JARs and then include them in my JAR as follows:
jar xf jakarta-oro-2.0.5.jar
jar xf jasperreports-1.2.1.jar
jar xf iReport.jar
jar cmf mainClass Spec Remote.jar *.class org/ net/ it/
The extraction of jakarta... produces the org/ path, jasperreports... produces the net/ path and iReport ... produces the it/ path. All are in my working directory as are my *.class files. I hope this is the answer you need.