You can model the structure of your Java application (including EJBs, Servlets, and JSPs) in a PowerDesigner OOM and then generate an Eclipse Java Project in which you will complete the implementation of the classes, and from which you will compile, package, deploy, and debug the application.
You can use the PowerDesigner plugin for Eclipse to enable round-trip engineering for Java development:
Perform high level analysis and design using PowerDesigner
Design and create Java components in PowerDesigner
Finish the implementation of Java classes within the generated Eclipse project
Compile, package, deploy and debug the application
Reverse engineer the final Java code to synchronize the PowerDesigner model