I just visited the site you designed, it's very nice. If you migrate your site to J2EE based, especially by using JBoss, it will be a real world proof of JBoss.
Okay, i'm comming to your point.
To Develop a complete J2EE based eCommerce application you should be very clear about the J2EE Technology. To get more ideas, just explore the http://java.sun.com/j2ee/ site.
People are so great, they made the J2EE Blue print program, the Petstore project available to JBoss, called it xPetstore.
Once you clear with the J2EE technology, download the JBoss and Xpetstore and explore it. It may be a kickstart for you with JBoss.
Use the Lomboz plug-in with Eclipse to develop and deploy J2EE modules.