Since you are new to web applications, my recommendation is to use a text editor and build your web application by hand. There are resources that will guide you through this, such as
http://www.moreservlets.com/. That is a fairly old resource but it will teach you the basics, especially how a WAR file is laid out and how the parts of it work together. And how to deploy it to a
servlet container.
The problem with relying on Eclipse when you are trying out a new
Java technology is that when Eclipse screws up (and it does that fairly regularly), it you do not have the basic understanding about the technology, then you will be completely lost. Personally, I use Eclipse as a glorified text editor and use other mechanisms (
Maven, Ant) to do my builds and deployment of web applications.