FWIW, we finally got everything pretty much arranged and I'm quite happy with the sound. Without the parts together and things in strange places as we were building the room there were moments when I was wondering, but after doing the calibration and everything, it's much nicer than we had before. I haven't noticed any problem with the balance or whatnot.
We did another strange thing, the back post isn't conducive to all speaker sizes so I decided to try the polk center/front low profile speakers mounted sideways at an angle for the surround. I was worried they wouldn't have enough bass, but everything seems to work pretty well.
So, what we ended up with:
3 Polk S55 for front and center (6.5" driver)
2 Polk S35 for surround (with 3D printed bracket to get an appropriate angle) (only 3", but it fits)
4 Klipsch CDT3800 CII 8" for atmos (ceiling)
1 Klipsch 10" sub. (It was easy)
I did keep the old Polk bipolar speakers, but the S35's (with the 8" atmos) seem to do just fine.
For me the real test is "are you in the movie?" We finally got everything arranged, got the screen up and sat down to watch stuff. There are all those questions: Is the screen bright enough? Can we hear the atmos? Are the behind-screen speakers too muffled? Is the sub doing OK? Is the dialog OK? (Our old setup we sometimes had trouble)
It was immersive. After about a minute I forgot all about those questions and just watched the show. That seems like how it's supposed to work