If you are not sure what to do and are starting from scratch then Maven can help get you started.
By following the the below steps you can get a new war project setup perfectly in eclipse.
mvn archetype:generate
mvn eclipse:eclipse
mvn package
or deploy it by setting up a server in eclipse and simply adding adding the project to the server.As some others have said the downside of using maven is that you have to use the maven conventions. But I think if you are just starting out, learning the conventions is a good idea before you start making your own. There's nothing to stop you changing/refactoring to your own preferred method at a later point.
Hope this helps.