For js2dkee, you have to set the j2ee.jar file in the class path before compilation and for BEA Weblogic use Apache ant to build the application.
Before deploying EJBs on Weblogic, you should create a .ear file with all the files needed for your Enterprise application namely ejb-jars (contains the ejb, home and remote interface) and war files (web applications contains jsp files, servlet class files and other resources). Then lanuch your weblogic server using the batch (StartWLS.cmd) file. After your server started, use this link in your machine http://localhost:7000/console
to launch the console, login and select your domain and then the ear application (.ear file) that you want to deploy.
More information read http://e-docs.bea.com