For a previous layout, I covered a regular-type basement window completely, using extruded styrofoam to cover the entire inside of the window and its frame, then covered that when I Installed the Masonite backdrop. From the outside, it looked fine (light blue) and the foam provided extra insulation. From the inside, you'd never know that the window was there.
The Milwaukee Road Warrior
...Natural light is always nice...
Well, it can be, but I prefer artificial lighting because you can have complete control of it. If you want to photograph your work in sunlight, build a portable diorama for that purpose.
The other advantage of covering the window completely is that no one can see your layout - it should be viewable only when you choose to display it to others. Otherwise, it's simply a temptation for theft or vandalism.
When I built my current house, I deliberately had no windows put in that basement room, nor is there any heating or cooling necessary, so no place for ingress of dirt and dust other than what's brought into the room through the door, and nothing for anybody outside to see.
The Milwaukee Road Warrior
...My backdrop will be 3 - 4 feet tall, which will leave very little window exposed....
I wouldn't leave any of the window visible from inside of the room.
My backdrop is mostly drywall extending from the floor to the bottom of the ceiling joists, but most of the room's 10 corners have been "coved" to create the appearance of a seamless background. The Masonite coves extend from the layout's varying heights to the underside of the suspended ceiling....

There's a "Layout (room) tour, with lots of photos..."HERE if you wanna kill some time. 
Wayne