General Questions + looking for good beginner's tutorial

Hello,
I'm a web-developer with some hobbyist-level experience in programming Java applications.
I'd like to write a content management system for my own clients, I was going to go with PHP, but thought I'd try it with Java instead. So the first step is to learn the Java web technologies! I'm pretty comfortable with the Java programming language, but I'm a complete novice when it comes to the Web APIs.
After some messing about, I've got Tomcat 6 running in Linux, and have played around creating a few JSP 2.0 pages. My first impression is that it seems incredibly complicated to do something that would be very simple in PHP: I have to define a tag in an XML library, and create a whole new class & object, using "magic" methods etc., just to output something very simple. I actually had a look at the JSP 1.2 examples, and they looked to me much simpler and more intuitive, with the code written inline in the HTML, much more like PHP. That makes more sense to me, but I suppose I should make an effort to learn the newer technology? Should I be using Tomcat 7 to learn instead of Tomcat 6?
I also had a look at the Java Servlet examples. These make more sense to me than JSP too. JSP pages just seem to be adding an extra layer of complexity on things with custom tags and tag definitions, etc., and I can't quite understand why. Maybe I will when I'm more experienced...
Can anyone point me towards some good tutorials that start at the beginning. I've pieced together what I've been able to figure out so far from the Tomcat 6 documentation pages and by experimenting with the structure of the various xml files included with tomcat, as well as copying the structure of the Tomcat 6 example pages. I've tried doing google searches for tutorials, but they all are either very out-dated (circa 1999), or they assume a whole bunch of knowledge.
I have learned a lot by experimenting with and re-creating the Tomcat 6 examples pages, but a good, simple, not-too-technical, beginner's tutorial would be a great help in "tying it all together" and removing some of the "magic stuff".
Thanks very much for your help.

The reason we separate projects into layers is because project grow over time to a point where its impossible to maintain if we don't separate it into modules.
Here is a post I provided on my opinon on coming up to speed on your first web development project.
http://forums.sun.com/thread.jspa?threadID=5433317&messageID=10960943#10960943
Here is a MVC design approach to your first project.
http://forums.sun.com/thread.jspa?threadID=5435833&messageID=10972163#10972163

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