I like your very common sense approach to this. I was impressed with the review here for the Pinnacles. For the money, could easily become one of the best buy’s in audio! I think the difference with the B&Ws will be viscerally noticeable.
For Center and Surrounds, I like the idea of the Ultras over the Primes... especially Ultra Bookshelves at Surround.
Get your 5.2 system dialed in before adding Atmos. Not meaning to discourage you, but the added complexity will make dialing in your base layer that much more difficult.
Amps are always a touchy subject, but think adding an amp for your front three is ideal. The Surrounds,Rears, and Atmos won’t draw as much power as those. I would spend wisely on a good 3-channel amp that will allow you to meet your SPL goals at your LP.
For 15x20... you might want to be prepared to add a third pb2000. Those dimensions may lend themselves to some tricky room acoustics. A third sub properly set up using a miniDSP 2x4HD and REW will really clean up any potential Bass issues. But DO start off with the two you have. Adjust if needed.

Also: do the subwoofer crawl to find the best places, acoustically, for your subs!
Cheers!