1) You can publish your script to an EXE by selecting
File -> Publish as EXE from the menu. Just follow the on screen instructions from there.
2) Here is some code that will resize the main window so the second window does not cover it up. I also added a background window that will fill up the rest of the empty space in the window.
Code:
#Add window to top
top_view = viz.addView()
top_view.setPosition([0,10,0])
top_view.setEuler([0,90,0])
top_window = viz.addWindow(pos=(0,1),size=(0.2,0.2),view=top_view)
#Reduce size of main window
viz.MainWindow.setSize([0.8,1])
viz.MainWindow.setPosition([0.2,1])
#Add background window
background = viz.addWindow(pos=[0,1],size=[1,1])
background.setView(view=viz.addView(scene=viz.addScene()))
background.drawOrder(-10)