mbucknam,
so first step is to add servlet-api.jar and jsp-api.jar to the build path (sounds like you did) and then either get the source from the Tomcat installer (Custom Install->Include Source) or download it then unzip it. The soruce unzips to a dir structure. In side of the “jakarta-servletapi-5” directory there are two dirs, one for jsr152 (JSP 2.0) and jsr154 (Servlet 2.4). You need to attach source to the servlet-api.jar file to the jsr154/src/share directory and the jsp-api.jar to the jsr152/src/share directory. This way the “javax” dir in the source folder maps up with the “javax” package in the root of the JAR file you are attaching to.
Now you should be able to debug servlet and jsp classes in Tomcat.
Now assuming you meant some other part of Tomcat, use the information above w.r.t. whatever JAR you are trying to debug.