As far as the overflow goes, I think you guys are extrapolating this to god only knows what types of flow. I ahd a single 1.5" drain/durso in my previous 360g tank and I had about 3000+ gph going through it just fine with a little more room to go too. A single in each box should be more than plenty and then some to get it done unless you are trying to pass some ridiculous amount of flow through there unnecessarily. For a tank your size going above 3500-4000 gph through the sump will be totally unnecessary and actually give you a tons of microbubbles regardless of baffles, be inefficient, and give you a ton of salt creep everywhere. I would use a single pipe as a back up and use the other to route cables from lights and such to the under side of the tank. You may even use it as a secondary close loop intake by routing it back to the tank.
As far as settling areas and such with your flow arrangement, if you are having sand put in settling is a mute point. you don't want to have flow blasting the sand as it will blow everywhere, land on your corals, irritate fish, and will tear up the seals in your pumps. Concentrate the flow to areas around the tank reminding yourself of where corals will be. Given you did it in locline, it should be pretty easy to adjust as time goes by.