Depending on the application, it could be stored in the registry, in a .ini/.cfg file in the program directory, or some sort of flat-file database, an embedded database like SQL Lite, or in a .dat file -- it could be anywhere, really.
Your best bet would be to contact support or the community for this software and find out where it's stored. If that's not possible, you could certainly poke around for yourself and see if you can find it. If it's a registry key value, you could easily push out a Group Policy or a login script to run a .reg file that would update that value for you. Editing a configuration file is a bit trickier -- you'd have better luck if the configuration file is identical for each machine because you could just copy and overwrite the existing config file with the new file.
What's the setting you need to change? If it's a hostname you might have better luck creating DNS CNAME in your DNS Server.
Do some digging and come back with more information and we can assist you more.