Controlling one window in an application is the same as controlling two or more windows in an application.
There is no such thing as a window signalling another window. Your application will be receiving signals from multiple sources. This includes keyboard clicks, time outs, button clicks, various interactions on the windows etc. If you want more that one window just build the windows, connect the signals and show them then enter the GTK main loop. Your application then processes the signals and does what is needed and display within the window.
Look at http://pygtk.org/
and then into the tutorials to find out more.