This isn't really Tomcat specific and would do better in the Servlets forum.
In my signature, there is a link to the servlet spec. In it you will find a very good description of the directory structure that a web app needs to have.
Also, if you go to our CodeBarn, under the servlets section, there are sample applications, packed as war files that you can simply drop into the webapps directory of a running instance of Tomcat. They will be unpacked and deployed to your machine.
You will then have sample web applications running on your machine that have a proper directory structure, and deployment descriptor with mapped servlets.