If you're new to Java, I'd work through the Java tutorials first.
The best place to start is here:
http://java.sun.com/docs/books/tutorial/index.html
This is especially important if you are new to object oriented programming. If you know C++ or some other OO programming language, you might be okay. But every language has its quirks and Java is no exception.
Although JSC has many nice features, it is not a good place to start if you are new to Java.
Also, JSC is being replaced, so instead of JSC you should go with NetBeans and the Visual Web Pack add-on.
Note that I started developing web apps with JSC six months ago, so I'm still using JSC. I can't speak to the differences between JSC and NetBeans, although I've read that the two are similar.