I was able to do this with Eclipse. I was running Jetty as an app-server. First, you should configure and enable support for your app-server in Windows/prefs/MyExclipse/Application Servers.
What I did then was deploy my .war file and run Jetty through eclipse. I could then hit servlet (but not JSP) breakpoints.
You need to start your server in debug mode and place breakpoint in the JSP,Java code. Go to debug mode you will get the server name and its status.(started,stopped)Right click on the server name and click on debug.By doing this your server will start in debug mode and with the help of break points you can debug your application.