The bulk of the configuration information about GlassFish Server resources, applications, and server instances is stored in the domain.xml configuration file. This file is the central repository for a given administrative domain and contains an XML representation of the GlassFish Server domain model. Default location for the domain.xml file is as-install/glassfish3/glassfish/domains/domain-name/config. For details on the domain.xml file, see Oracle GlassFish Server 3.0.1 Domain File Format Reference.
The logging.properties file is used to configure logging levels for individual modules. The file is located in the same directory as the domain.xml file. For further information on the logging.properties file, see Setting Log Levels.
The asenv.conf file is located in the as-install/glassfishv3/glassfish/config directory. It's purpose is to store the GlassFish Server environment variables, such as the installation location of the database, Message Queue, and so on.
Changes are automatically applied to the appropriate configuration file. Do not edit the configuration files directly. Manual editing is prone to error and can have unexpected results.