Directory Server stores server instance configuration data in files, but the configuration data is also accessible over LDAP.
The files are stored under instance-path as follows. Directory Server stores the LDAP schema, which define what directory entries can contain, under instance-path/config/schema/. See Sun Java System Directory Server Enterprise Edition 6.1 Man Page Reference for reference information about the schema, and Chapter 11, Directory Server Schema, in Sun Java System Directory Server Enterprise Edition 6.1 Administration Guide for instructions on managing schema. Directory Server stores other configuration information in the dse.ldif(4) file, instance-path/config/dse.ldif. Avoid updating this file by hand.
Over LDAP, the schema information is accessible under cn=schema. The other configuration information is accessible under cn=config. In practice, you do not generally update data under cn=config directly. Instead, you use either the web based Directory Service Control Center, or the dsconf command. Both Directory Service Control Center and the dsconf command change Directory Server over LDAP. Yet, both also spare you much of the complexity of making configuration adjustments with LDAP modify operations.
Almost all Directory Server product documentation is devoted to Directory Server configuration. In Sun Java System Directory Server Enterprise Edition 6.1 Administration Guide, you find extensive instructions for accomplishing a variety of tasks using command line configuration tools. The Directory Service Control Center online help can help get you back on track when the Directory Service Control Center interface does not seem intuitive enough.