You're better off not using an IDE until you're comfortable doing this by hand.
On Tomcat's site, there is a tutorial called First Web App which takes you through all of the steps for writing and deploying an application in Tomcat.
This is a good place to start.
Also, our CattleDrive has a section on Servlet/JSP developement which explains in great detail how to deploy an app in a
servlet container.
At the moment it uses Orion but there's been talk of switching it to Tomcat.