Twin thrusters is a thumbs up from me. That will give the opportinity for both mix-master and gyre settings.

My only caveat would be under the rocks. What I would suggest you consider is an over-the-top closed loop system. Since you have the thruster area sequestered, you could go over the top (avoiding holes in the tank) and down to the bottom with closed loop pipng. Then position eductors throughout the tank bottom to keep the detritus in suspension. This is IMO the biggest problem we face. The accumulation of detritus under rocks, in the sump etc. is a time-bomb waiting to go off.
Advantages of this closed loop?
1. The pump(s) is outside the water. This keeps the heat impact down.
2. The pump(s) can be easily removed for servicing or replaced for failure.
3. Using a 220+V pump on a VFD (Variable Frequency Drive) would allow you to control the flow and not only stir up more detritus, but also give a "sleep" mode.
4. In my next build, I will use two of these on opposing ends of the tank to make a bottom wave/surge. Varying the flow back and forth, slowing it for night-time, and blasing the reef periodically.
Yor design lends itself well to this application.