To do any changes to WDJAVA based applications, you can use NWDI which is get it installed along with EP or NWDS which can be installed on individual system. Since NWDI is license dependency. so we use NWDS for any customizations to WDJAVA applications.
You have to take a copy of that application and import to NWDS and do changes as per your requirement and redeploy the custom. one.