Softimage sets the variables that it needs in its environment script: the setenv.bat file on Windows or the .xsi_2011 file on Linux. This file is run or sourced before launching the interactive Softimage application, the command-line Softimage application, or the mental ray renderer.
The environment script is created when you install Softimage. It usually does not require modification, but advanced users can modify it, for example, if they need to accommodate specific aspects of their network.
Because the variables are all set in the environment script, any modifications need to be made in only this one file. In addition, because the environment script is run only before launching Softimage, any variable settings will not interfere with other applications or even with other versions of Softimage on the same computer.