You have to set a breakpoint in your code. This can be done by doubleclicking on the left margin of your Java src file editor. Once you run the application the debugger is invoked and you have to switch to the Debug Perspective in eclipse which it does by asking you to switch to debug perspective once it encounters a breakpoint.
Use eclipse help tool to for more information on the Debug perspective.
Also, I think you have to setup your project as a tomcat project.
A less pleasant way to get the same effect is to start a copy of Tomcat with Java Remote Debugging turned on and connect as a remote debugging session.
I recommend sysdeo. It's a little frustrating to get started initially - especially if you already have your webapp defined in Eclipse and have to go back and manually the make connections that would be done by the plugin when you create a new webapp with sysdeo already installed, but the end result is worth it.
I'm going to be a "small government" candidate. I'll be the government. Just me. No one else.