Broadly, there are two kinds of application security:
In programmatic security, application code written by the developer handles security chores. As an administrator, you don't have any control over this mechanism. Generally, programmatic security is discouraged since it hard-codes security configurations in the application instead of managing it through the Java EE containers.
In declarative security, the container (the Enterprise Server) handles security through an application's deployment descriptors. You can control declarative security by editing deployment descriptors directly or with a tool such as deploytool. Because deployment descriptors can change after an application is developed, declarative security allows for more flexibility.
In addition to application security, there is also system security, which affects all the applications on an Enterprise Server system.
Programmatic security is controlled by the application developer, so this document does not discuss it; declarative security is somewhat less so, and this document touches on it occasionally. This document is intended primarily for system administrators, and so focuses on system security.