To facilitate mass deployment, settings can be changed from command line, by importing a configuration file. The configuration file can be in Property List or JSON format, whichever suits you more. The default configuration files in both formats are attached to this article: take one of them, edit as needed and erase settings that you don't want to change.
To apply the file, let your deployment script invoke the following command:
/usr/bin/open -gnW -a /Applications/Preproxy.app <path-to-preproxy-configuration-file>
Providing SetAutostart=true will also automatically start the service.
The configuration UI should not be running while executing this command, because it will revert the applied changes upon exit (having the service running is OK).