Re covering with wing up vs down, California Car Cover's website asks for Make, Model, Year, and then Trim which gives these 2 options: "Base With 2 mirror pockets with wing deployed" or "Base With 2 mirror pockets with WING RETRACTED (Ford recommends storing car with wing deployed. Choose option with wing if you intend to store car with wing deployed.)"
https://www.calcarcover.com/custom-fit-car-truck-covers/ford-gt-car-covers
https://www.calcarcover.com/custom-fit-car-truck-covers/ford-gt-car-covers