Simply assemble the Service:

public void assemble( ModuleAssembly module )
        throws AssemblyException
{
    module.services( EmbeddedDatabaseService.class );
}

The embedded Neo4J database files are stored in the data directory defined using the FileConfig Library.

@Service EmbeddedDatabaseService neo4jService;

public void doSomething()
{
    GraphDatabaseService db = neo4jService.database();
      [...snip...]

}