Clarification:
J2EE has an additional E in it, while J2SE as an additional S.
Ok, now that we cleared that up, Lets see if I can answer your question.
There is no magic button such as 'java web start' that will automatically generate computer code for you. You have to write java line by line and debug each and every line of code. A typical whole project may consist up up to 1500 functions (mine has over 12000). You read whole books on the subject as I discuss below and work through thier examples. Within about 2 or 3 years of hard study, you should be a pretty good programmer.
Java is an object oriented language that you'll need to become familiar with that takes some practice to learn. Also, a java based web site consists of several technologies in addition to the java language that you'll need to be familiar with. Many programmers will read articles on the internet and pick up fragments of information on these various technologies and throw a web site together thats impossible to maintain and enhance. I think it would be better if you read whole books and experiment with the technologies. Consider it an at-come college course. Here is my suggested reading list read in roughly this order ( I suggest buying them one at a time via the internet (its cheaper) before moving onto the next book).
"Thinking In Java" - Bruce Eckel
HTML & XHTML: The Definitive Guide
JavaServer Pages - Hans Bergsten
Programming Jakarta Struts
JavaScript: The Definitive Guide
SAMs Teach Yourself SQL
JDBC and Java
Also, visit the Web Tools Platform (WTP) Project (www.eclipse.org/webtools) . Its a free Eclipse Java development tool that has the bulk of the java development IDE market (above even JBuilder).However, I suggest creating a few small java programs using the dos command line before you let this IDE do a lot of the work for you. You also might want to install some type of database (Oracle Lite, MySql, etc) on your computer so you have a database to play with (you'll need a computer with at least 2Gbytes of memory).