I don't think there is any one book or website that will teach you all those things. Most things are focused one either one or two specific topic. There are some books that try to teach all the different things in the major parts of
Java EE, but I find that they do a very poor job on explaining them since they sacrifice detail for number of topics covered. If you want the best possible learning material for Servlets and JSP, read the Head First Servlets and JSP book. The book is worth every penny.
If you don't want to spent any money, the best thing to do is google for specific technology tutorials, i.e.
struts2 tutorial hibernate tutorial