Thanks in advance.
I would say you're on the right track. I think having the Definitive UIW RLS II for your LCR makes sense - I have the in-ceiling version of these in my showroom and am very-happy with them. Only comment is it's always preferable for the centre channel to be vertical. With a room your size I'd consider an acoustically transparent screen & projector to make this happen. I'd stick with the RSS II in-ceiling for the surrounds and rear channels as the bipolar design will create a greater sense of envelopment. Your ceiling height is not the greatest for ceiling speakers (your ceiling is fairly high!) but for surrounds I think it should be fine (yes, it would be preferable if they're in the wall a few feet above your head when seated). Five feet away from the sofa is plenty especially given how high up the rears are. I have two RSS II surrounds in-ceiling in a 10 ft ceiling and am very happy with their performance. I would also put at least two (preferably four but I know that can get expensive) inwall subwoofers for bass.
The drawing helps to see what you're dealing with. The archway and brick arch are not ideal for sound as they introduce the potential for ambient noise and unbalanced first reflections. Keeping that in mind we have to manage the best we can, like the majority of media rooms. Also, having a couch is good for sound absorption - and a carpet floor (or rug) would help too. I think the placement you're talking about for the surrounds makes sense - I positioned mine so one dipole fires at the wall and the other at the couch. Putting the subwoofers in the cabinet sounds like a good idea, and two should help with seat-to-seat consistency. Also make sure the LCRs are parallel (i.e. don't put the centre closer to the seat than the left & right), and spread out enough (a rough rule of thumb is the left and right speakers should be as far apart as the seating position, which would be 12-13 feet from your drawing).
Regarding the motorized screen, another option is something like the Black Diamond from Screen Innovations. Works very well with ambient light and descends out of the ceiling to your desired viewing position. This could eliminate the need for the flat panel TV, although you can still have both and have the flexibility to watch afternoon sporting events etc.
Sorry, I was under the weather for a few days. The book case sounds like a good idea... I'd love to see a picture once it's all complete! I think the placement of the surrounds makes sense, given the challenges your room presents. As for the subs, when working with two, my first choice would be to put one at the back right of the room, and one at the front left of the room, or alternatively put one sub on the left wall, and one on the right wall, staggering them so we expand the sweet spot. In a full-blown custom theatre I recommend four subs (one for each wall), but media room's can be more difficult to achieve optimal placement.
In this case I would probably opt to make use of the book case and put one sub between the left and right speaker, but you are right in that the disadvantage is once it's built there's no way to move the subs around to improve bass performance. I would also make sure I thought through what it was resting on, and put sand or insulation beneath it depending on the way it's installed in the book case. If you decide you can live with subwoofers in the room this is safer from an audio perspective, as it will allow you to "kick" the subs around the room to find the best placement. Technically speaking, it's always a good idea to have a formal analysis done to identify the weak spots in the room before you start installing; I have this done for the custom home theatres that I design and build. That being said, the rules of thumb can work out nicely in most cases.