Environmental information required for configuring a data storage system for using a file mapping protocol is collected and qualified via a spreadsheet used as an input file to a configuration program. The configuration program provides a comparison of the present configuration to the new configuration specified in the spreadsheet, and provides to a system administrator an option of applying or skipping the new configuration for each of multiple classes of configuration objects including iSCSI targets on storage array controllers, file server interfaces for host access to file mapping information, file systems, and iSCSI clients on the host processors. Once the system administrator approves the selected configuration changes, the configuration utility produces a series of control commands for execution by a control command interpreter of a file server in order to change configuration settings in the file server and in the storage array controllers.