are built and designed with the horizontal wings that fill in a window that opens and closes vertically.
Being a horizontal situation, you will have to fill in the area ABOVE the window unit with painted masonite siding, or possibly you could contact a contractor to build a window case for the area above the AC. I would do that if I was contracted.
The other question, the screen will have to go. Your immediate concern is mounting of the AC and making the window secure again and securing the AC unit also.
Remember on horizontal AC units, the window closing down on the unit acts as support and keeps the AC in place. In your case you do not have this and this is why you need a good carpenter to window frame the area in and secure the AC.