If I understand correctly, our WS (Web start) app will need to interact with the server (eg sending http requests), so your web app (server side) will need some classes to.
Basically you should split your classes into 3 jars :
my-client.jar contains the classes only needed by the client
my-server.jar contains the classes only the server needs
common-resources.jar contains the classes both need
my-client.jar and common-resources.jar must be added to your JNLP file and you must put it in the war with all your static content (images, html, js...)
my-server.jar and common-resources must be declared in your ear descriptor (application.xml) and you should put it in the ear.
Separating client side and server side code into distinct jars prevents clients from downloading critical classes (eg servlets) and/or configuration files which might be a vulnerability for your server. Never trust the client !