Any configuration would end up updating the system registry. If it is the registry, you can export the entries to a .REG file and import it as a part of Setup. You import a .REG file by just opening it (like an EXE file). You can have Windows do this once on start up and force users to restart the machine.
Another way is to make the appropriate system registry entries using Setup. InstallShield supports both approaches. If you are using Setup Wizard then you take the .REG file approach but the users will have to explicitly open the file (or you can tinker the Setup kit source to do it.)

HTH,
SUN.