What you described "Trying to upload an illegal jar archive. Make sure the archive file contains the descriptor file ejb-jar.xml." did not make much sense to us since we have never seen such error message on a normal installation.
What is your operating system? Is it Windows? What program are you using to "open the .jar file"? It is supposed to be executable if JRE is installed and you only need to double-click on the jar file. Or you can double click on the .bat file to start the TRiLOGI software.