The Simulator for Arduino IDE has several sections. These are:

The order of the Program window, Variables are and Arduino picture may be swapped by Selecting View|Arduino on Left. The preferred method is to have the Program Window on the left so that the work flow is input,data and output. The Arduino picture and/or Variables area may be hidden by selecting Options > Show Arduino and/or Show Variables and clicking on it to uncheck these options.

When the Simulator for Arduino IDE is resized, the Variables window will disappear first since this is seen as the least important window. If the main screen is made smaller, the Program window will then disappear and the Arduino Screen will always be on top. This allows for sketches to be simulated as they would appear for real. There is also a Minimize button designed  for this purpose.

Note that the Variables Area and the Arduino picture can be undocked by using the Allow Dock/Undock in the Variables Area right click popup menu.