I assume you have different config files. At runtime the value of $APT_CONFIG_FILE determines which file is used, either the default as set in DSParams or a value passed in to the job with this parameter.
we are using the config file mentioned in the administrator... there the correct config file only we have mentioned.... but some dataset data files are going to the default installed path location for datasets... like /datastage/IBM/InformationServer/Server/Datasets but we have mentioned in the config file the path.... /Data/rsrc