Jackrabbit's main configuration lies in the so-called repository.xml file. It contains global configuration such as Login and Access Management, Versioning or Clustering. Then it defines how the actual data for a certain workspace should be stored by choosing a PersistenceManager and what search/query implementation to use by defining a SearchIndex.
For each workspace that was created, there will also be a workspace.xml file created inside the workspace home directory that will be used for the workspace - these files have to be changed, too, because the workspace-specific configuration inside repository.xml is only used as a template for new workspaces, ie. if you use the createWorkspace of the Jackrabbit API, the workspace.xml is just a copy of the Workspace element inside repository.xml. You can also manually create the workspace folder with a workspace.xml file to create a new workspace yourself (Note that depending on the persistence manager you will also have to setup a database and configure the access to it).
The default configuration of Jackrabbit can be used in many cases. To find out more about configuration options, see:
Jackrabbit Configuration: Configuration files and variables
PersistenceManagerFAQ: Persistence manager and file system configuration
DataStore: How to configure and use the binary data store
Clustering: How to set up and use clustering
Search: How to set up and use search
RepositoryLock: How to configure repository locking