The JavaTM 2 Platform, Enterprise Edition (J2EE) defines the standard for developing multitier enterprise applications. J2EE simplifies enterprise applications by basing them on standardized, modular components, by providing a complete set of services to those components, and by handling many details of application behavior automatically, without complex programming.
You will need to read the rest of the story to fully understand the power that J2EE technology has to offer. Once you understand the solution that J2EE can provide for every eBusiness application, you can start building the rest of the puzzle through the many Java resources that are available to you.

Once you have a candidate for a J2EE application you need to start piecing it together in a design and determine which pieces fit where and why you're using those pieces. This website shares many example of how to build a multi-tier J2EE application and how those tiers exist and function together as an application:
Sun's J2EE Development Guide
J2EE Architecture
What is in a J2EE Application

When designing an application from scratch you will often find that you don't need to do too much actual work from scratch. There are many open-source frameworks out there that can be used to easily piece together a multi-tier application. You could write everything from scratch - but why?