I have j2ee web project in IntelliJ IDEA with complex web resource directory structure
Where to find the equivalent of this setting in Eclipse?
First, make sure that you have Java EE development portion of Eclipse installed. The easiest way is to download "Eclipse IDE for Java EE Developers" packages from http://www.eclipse.org/downloads. Next, make sure that you've created a "Dynamic Web Project". Finally, go to Project Properties -> Deployment Assembly.
If you don't see Deployment Assembly page, you are using an old version of Eclipse. There is a way to do this in the older versions, but you will be happier if you upgrade to the newest release. See link above.