Open Safari, set the window the way you want it then quit. Open Safari again and the window should be the way you just set it. Now open a second window and set that the way you want it, close it and open a new window and it should be the way you just set the second window. When you're using Safari and open another link, if it opens a popup or another window at a different size, then the next time you open a second window, it will open at the same size/location as the last window that was closed.