I often find myself in the situation that I want to read or edit stuff down below at the end of the the properties-column (or designer-area).
Which means I have to collapse the output-window.
Now there could be different solutions how to handle that situation.
Maybe you could make the window only draw below the designer-area and not the properties/events-column.
Or you could move the drawing-area of the designer and property-window above the output window, so they will never be overlapped by the output and instead move upwards as soon as the output pops up.
Or maybe you could add an icon to pin the output down, so it doesn't automatically pop up if the users starts the application.