To make a VSE JCL configuration file available to MSS you specify its location using the VSE_STARTUP_CFG environment variable. For example, if you create the configuration file in c:\setup\vseconfg.cfg (on Windows) /home/setup/vseconfg.cfg (on UNIX), you would set VSE_STARTUP_CFG as follows:
SET VSE_STARTUP_CFG=c:\setup\vseconfg.cfg
VSE_STARTUP_CFG=/home/setup/vseconfg.cfg export VSE_STARTUP_CFG