I'm sure you have a good reason, but why can't you build a wall on that side of the theater? Enclosing your HT would make things a lot simpler. It would be pretty easy and inexpensive to build a 2x4 wall and drywall it. You could always take it down if you wanted later if you sold the house or no longer wanted a dedicated HT room.
My opinion is that mounting your speakers in columns (on on/in the wall if you build a wall which I recommend) would be better than ceiling mounted for surrounds. I think mounting them in the ceiling would really get in the way of the Atmos effects.
I'd prewire for 9.x.6 if you can - It's easier to do it now even if you don't use them all now. I agree with Oria34 that I would do 4 Atmos speakers instead of 2, even if I had to do a 5.x.4 system rather than a 7.x.2 system.
Instead of in wall speakers for the L/C/R what about using an acoustically transparent screen and putting your speakers behind it? It's a clean look and the sound actually comes from the screen so it feels more natural. That would open up your speaker choices a bit as in-walls are excessively expensive for what you get. That being said if you need in-walls, Triad seems to be well thought of.
You will need acoustic treatments to get the best sound. I think you want roughly 1/3 reflection, 1/3 absorbtion, and 1/3 diffusion. Acoustimac sells panels with Owens Corning 703 or other acoutical treatments (for absorbtion) pretty inexpensively, and even materials for DIY if you prefer. Don't skimp on the treatments as the room makes more difference than any speaker or componant.
That's a good size room, and if you leave it open to the rest of the basement a HUGE space. IMO, the PB2000 would be marginal if you close it off, but no where near enough sub if you leave it open. Subs will try and fill the whole space. Look at DIY for options here, as you will need some major output.
You'll need a bright projector for that size screen and a completly light controlled room.
Paint the walls and ceilings dark colors and use black velvet where possible.
7.4.4 Theater Room: JVC-RS500, Silver Ticket AT 2.35:1 142”, Onkyo RZ830, Anthem PVA-7, Panasonic UB420, Apple TV 4K, JBL Studio 530’s, 4 - 15" DIY Sealed Subs
3.1 Living Room: Samsung 64” F8500 Plasma, Anthem MRX 300, Dynaudio Audience 52’s, Dynaudio Audience 122C, NHT SubOne, Roku Express (2019)