Have you figured out how to make the fish room bigger yet?
I would DEFINITELY figure out your water change plan before getting too much further with the tank. Automating it would be awesome, but barring that, at least make sure you build a system that will make it easy and not too time consuming.
My systems are small, my RODI is in another building, and water changes are my biggest chore (acutally a real PITA) and I SO wish I had a plumbed in water change solution.
Lastly, I'm surprised you've made it this far along and you're not yet familiar with the Apex. With a 1,000 gal tank and all the associated equipment, a good controller seems like a necessity. If the consultants helping you design and build this system haven't already sold you on a controller, I would start getting nervous about what other details may have been overlooked...
Not trying to be a downer, but I think those three issues above are significant, and I'd slow down a bit and address them before life gets difficult.