I might be here completely wrong, but the proxy settings in Linux are stored in the http_proxy variable.. If that variable is set, then programs will use it as the settings..
For example, if one exports the variable:
and runs any programm requiring web, it should go through the proxy.
This does not answer your question though exactly (although if you place this line in your .bashrc file in your home, this might be a workaround for your problem).
I suppose you might need to extract the address/port from the pac file youself.. Access it from the browser and use the "save as" option..