In WebLogic Workshop 9.1 and above, we can create following directory structure create custom EAR application, which can be used under Eclipse.
Best Practices from (edocs.bea.com)
# Use the same source directory structure with your own J2EE application projects, so you can utilize the WebLogic Server build scripts to compile and deploy your applications. The following summarizes the contents of a simple source directory that follows the WebLogic split development directory structure format:
\myProject
\myProject\myEar
\myProject\myEar\META-INF\application.xml
\myProject\myEar\myEjb\com\*\MyEjbGenEjb.ejb
\myProject\myEar\myEjb\com\*\*.java
\myProject\myEar\myWebService\com\*.*.java
\myProject\myEar\myWebApp\*.jsp
\myProject\myEar\myWebApp\WEB-INF\web.xml
\myProject\myEar\myWebApp\WEB-INF\src\com\*\*.java
