LOL - Totally agree with Aberk. "Surround Speakers" in ceiling should only be done when that is the only possibly option even though you know you're not getting true surround.
First off, I'm jealous! We just bought a house (not custom built - I live in SoCal) so had to "make do" with the living room as is and it's not just a media room so much fewer options than you have. I did a 5.2.4 Atmos set-up and love it. With a dedicated media room, you could likely go 7.2.4 to take it all the way. (With my room the single long sofa is against the back wall so no room for "back surround" speakers.)
For me, there's a few things to think about...
1) Video (TV vs Projector)
2) Sound Set-Up (Not only what the set-up will be but just as important, what A/V Receiver and/or Amp, what speakers to get - skies the limit on price range here.)
3) How to set up the room in general
I'd start with "What will I use this room for?" Some people prefer a straight "cineplex" set up meaning 1-2 rows of cinema style seats (but nice leather comfy reclining ones of course). But that does limit the room to pretty much ONLY being used for watching movies or tv shows. You might consider a hybrid set-up, one that emulates the cinema experience but with furniture/layout that also allows it to be used as a den/family/gathering/party room - a place to also hang out and watch things like sporting events or other more casual viewing. So maybe you still go "two rows" but maybe a sofa and some plush recliners and such. It all just depends on what you want and how you want to use the room.
I would generally suggest having the double doors be the back of the room and the TV/Screen be on the opposite wall. It looks like those are the shorter walls giving you more depth in the room to have your seating and still have room behind for your surround speakers and such.
Other things to consider... With a projector, ambient lighting will make a huge difference - only the most expensive projectors do well with light in the room. Again, this may not matter if you only intend to watch movies/tv in the dark, but something to think about. The latest OLED TV's from LG are amazing picture-wise regardless of ambient light. On the other hand, they limit you in size a great deal compared to projectors. As with most things what is best will depend partially on how you want to use the room and watch stuff and also on what your budget is like.
For speakers and receiver, it depends a LOT on budget. I had a decent budget in my new home theater living room, but not unlimited expenses so I went with the higher grade of "consumer line" products. I bought the premium line of Polk Audio Speakers (their Signature Series). But I didn't cross over into the enthusiast class which the low grade of those type of speakers would cost more than I paid or could afford. At any rate, I love Polk and feel the sound I get out of them is excellent. On receivers, you have to decide to buy a receiver with built in amp (again, more consumer line way) or use a separate amp for sound amplification (the preferred enthusiast way). Really all depends on $$$. I bought the higher end "consumer grade" Denon AVR-X6300H. I don't have an external amp, just the Denon. Because I don't have surround back speakers, I was able to use those channels on the Denon to bi-amp my l/r tower speakers.
As far as speaker set up goes, check out the Dolby website - they have great diagrams that you can download in PDF that show the best set up for Dolby Atmos. Speaker set-up is key!!! Can't tell you how often I've gone into a house with a super expensive sound system, but it didn't sound as good as my old cheap surround system because they had it set up horribly. Because you have a dedicated media room, you can, and should, follow the Dolby Diagram exactly - it will give you the best result.
I'd definitely suggest in-ceiling speakers (4 of them) for your Atmos sound. I'd suggest nice tower speakers for your Left/Right (no surround w/great l/r is better than having surround with not great l/r - they are important speakers). Equally as important is your center speaker - it will carry most of the dialogue so get the best one you can afford. (Well, that's kinda obvious - you want the best everything you can afford.) But also don't get cheap on your surrounds and ceiling speakers - you want things to equal out.
Like I said, the sky really is the limit and you could probably spend as much on just your media room as you did your whole house if you wanted to so you have to first decide your budget, then decide what you're gonna use the room for, then get the best of everything you can afford to fulfill that vision - and make sure your speakers are set up correctly!
(If you're like me and have some money to spend but are somewhat limited, let me know - I got some great deals on all my equipment and saved myself several thousand dollars...)