Thanks for posting the photos. I think you are headed in the right direction. Members here in general try and dissuade the use of upfiring ATMOS speakers as the proximity to the main speakers tends to cause interference. The X15 is an excellent sub so no qualms there. I'll assume that the surrounds are slightly behind the two seats on the sides, or are they on the rear wall?
For ATMOS, yes, it would have been nice to pre-wire for two more ceiling speakers a little in front of your seats. I would stick with the two for now and if you get a chance to install two more in-ceiling that would be the way to go if ATMOS is important to you.
The proper approach is to concentrate on the bed layer first (fronts and surrounds). Windows and doorways are always constraining factors which has led to your main speakers being closer together than what would be recommended for that size of room. You want to have enough separation between the speakers to avoid interference between them. Some members will recommend that you forgo the center speaker because the mains are so close together. Using 2 in the front creates a "phantom" center channel and depending on the seating distance that can work quite well. You can experiment with your existing speakers by simply disabling the center speaker in your AVR setup menu.
Having said that, my speakers are also a little close together but I like having a center speaker to anchor the dialogue to the TV. My seating is spread further out, so it helps with the seats that are off to the side. The best centers use a 3-way design as that reduces comb filtering, which causes interference when you move off of the center axis. A good 3-way center can cost almost as much as the main pair though, which makes upgrading all 3 a bigger challenge.
Hardwood floors and windows make the room more lively but you already have an area rug, which is good, plus the soft furniture and window treatments help. A simple test is to clap your hands and listen for how long it takes the echo to decay. If it drops off quickly, then the room likely has enough soft elements to absorb the sound energy. Adding treatments can be a tricky business though.
I've rambled on here, so I'll talk about speakers in another post.
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