I have a project called onlinelib inside the webapps directory.
In the onlinelib directory I have some jsp's.
In the WEB-INF\classes directory I have a servlet class called HelloWorldExample where I create a database connection to derby and all my jsp's action element point to this servlet.
So this acts like the controlling servlet.
In the WEB-INF\classes\jbean directory I have a java bean class called BookSelectedforDel.
When you are describing your project structure, is this the structure of your source code? Or the structure of the results after compiling? I hope that it is the latter. For example, it is not a good idea to place the .java source files in WEB-INF/classes, instead you should place them in another directory such as src/main/java, and resources (JSPs, html, css, etc) should go in src/main/webapp.
Other than that, the typical steps are:
1) Compile the .java files (the .class files go into target/classes)
2) Gather the classes and resources into a central location (building and exploded WAR structure)
3) Packaging the WAR (from the directory built in step 2)
Google building war with ant will yield some examples, though some are overly complicated and many don't have the clean directory structure that Maven has.
Finally, use packages to separate your beans from your servlets.