The Data Integration Service accesses control files when it runs mappings that generate columns for flat file sources based on control files. When the Data Integration Service runs the mapping, it fetches metadata from the control file of the flat file source.
Use the Developer tool to configure the control file directory for each flat file data object that is configured to generate run-time column names from a control file. You cannot use the Administrator tool to configure a single control file directory used by the Data Integration Service.