I am considering the SC3DA soundbar with 2 Invisia HTR 7000's for rears, 2 Invisia 650's for front height, and 2 Forcefield 4s. Should this work well? What is the best placement of the 650's?

Sounds great, yes, we are recommending the Invisa 525 or Invisa 650 for the Atmos height channels. I believe Dolby has some information on preferred locations for their .2 and .4 Atmos height speakers they have just started to release.

Is it beneficial to use 2 different size subwoofers in an application where one (presumably the smaller one) would be on one side of a fireplace in a corner and the other would be on the other side of the fireplace along the wall in a large room?

Depends on how they are implemented, but the room's nodes will have much more impact than any subwoofer size difference. Since the 3D Array requires a higher crossover point, you are going to want to keep subs up front if possible. Corner placement tends to exaggerate room nodes too.