There will be some compromises in that set up but you have to work with what the room offers. If the front speakers will be in the built-in make sure that any ports are front firing, like the Debut 2.0 B5.2 that you have listed. Speakers work better when moved away from the wall and onto stands but it looks like that won't be an option with the built-in.
Same with the surrounds. They work best when at or a little above ear level, but looks like you won't be able to have them on stands in the room or mounted on the walls, so that leaves the ceiling. You shouldn't do in-ceiling surrounds and ATMOS together, so I think you're best to do 5.1 with surround channels as you have planned. Some might forgo the surrounds because you don't have ideal placement, but I think in-ceiling is better than no surrounds at all. That was also a compromise I had to make with my system and I enjoy the surround effects even though they are above.
As the room is large you might want to consider a better subwoofer. The Elac sub will fill in the bass that the bookshelves can't produce but at higher volumes it may lack enough output for that big of a room, and it's only rated down to about 30Hz. That might be ok for average music listening, but for movies and music with deep content you want a sub that will go down to 20Hz. Two RSL Speedwoofers would do nicely but if dual subwoofers are not an option consider something with a 12" driver like the SVS PB-2000 Pro or something from Rhythmic or Hsu. Other options from Monoprice as well depending upon budget, style and size limitations.
