Well, at a quick glance you're not using at least some of the functions right. The _setup() and _sync() versions of the .scene do not have to be called if you're using the _fade() for a scene. The _fade() function of your scenes will run the _setup() function if it wasn't loaded before.
Having said that, I haven't tried to make a scene fade in and fade out yet, but you're now using three functions that 'load' the scene already. You may want to open the .scene file in AppGameKit Studio and click on Script, next to where you Save your scene files. It will show you the code the .scene has generated.
If you don't want the scenes to change resolutions or windows, you most likely will want to run the function that ends with _create_window(0) to prevent that.