Well, big built-in tanks -are- somewhat involved and complicated! But assuming you are already into your house construction phase I wouldn't go off the deep end worrying about it. Here's something to think about: All those institutional display tanks seen at offices and other places have to be outfitted and maintained by somebody and usually its some regular old aquarium shop. Yes, there's probably somebody who knew what he/she was doing (probably a fair number of our members are professionals who earn money doing these sorts of services) but often they are then maintained by people who may not really know that much about them but can still do it. So there very well may be "canned sump systems" out there to be had or, as we've all seen from time to time on the web, there's a fair amount of web "how to" material out there I think with pictures and all of people designing and constructing sump systems. Or, perhaps its just a matter of lining up the right number of large external cannisters under that big tank and perhaps augmenting it with a few powerheads in strategic places. Definately you're going to want to be starting up a thread in the hardware section and trying to get the attention of folks over there. It may take a little longer but if you are just persistent, you may get some good advice over there both about what is really needed and about how to go about it.
~~waterdrop~~
ps. another thing I forgot to ask, maybe you said, was how high the tank walls are planned to be? If these get too high then maintenance can become a problem. I remember a few situations where some of the more illustrious members have had to use scuba gear for mainenance, lol.