I'm still settting up my first personal system, so take my opinion with a grain of salt. However, from all the research I've done, I would say the answer to your questions is, "it depends". It seems to me every single system I've seen has their system setup slightly differently, including the commercial operations. Perhaps a better question to determine configuration is what do you want to grow? Some plants do better in raft systems, others in flood/drain media systems, ect. This is a major consideration before deciding large vs. small, etc.
Also, I would suggest you take Sylvia's advice (from her book's appendix) and setup a small (personal) system first before considering a commercial system. This is what I am working on, and depending how it goes I may expand into a larger system later.
There is a ton of useful information available online about aquaponics, so I would suggest researching further so you can identify the factors most pertinant to your situation before starting in on a system design.