Jerry,
While there are some basic regulations, rules and guidelines, how you design your electrical system (batteries, charging sources, loads, etc.) really depends on what you want to accomplish (house capacity in amp-hours, inverter use, degree of redundancy, etc.) and how much you want to spend. The latter tends to constrain most of us...
Like your Commander, Trishna's 12 volt system includes two inboards (alternators & starters) and a genset (starter). I have a dedicated starting battery for each engine.... a total of three... and 2 6 volt Trojan's wired in series for a 12v house bank. While I'm not an electrician, I'd be happy to discuss design over the telephone to get you started.
Resources I strongly recommend:
http://www.amazon.com/Boatowners-Mechanical-Electrical-Manual-Calder/dp/0071432388
http://www.jackrabbitmarine.com/Categories.bok?category=Wiring+Diagrams+%26+Advice
http://www.askjackrabbit.com/
The first link... Nigel Calder's book... is, IMHO, the best place to start.
Cheers,
Scott