How about this:
Grid power goes through ATS to the main load center, which has a 2 pole 60A breaker sending power to AC1.  Inverters feed a critical load panel.  Generator's start circuit is removed from the ATS and wired to the inverters. 
 
Power outages transfer ATS to emergency power position, but cannot start generator.  Main load center is not powered, but the inverters feed the critical loads.  At a programmed voltage or amperage point, the inverters start the generator, which feeds thru the ATS to the main load panel and therefore AC1 for charging.
 
Possible problems:  too much load on main panel to leave power for charging. 
 
Also, does that ATS sense generator input and executes a time-delay before latching,  or does it latch after a time delay from losing grid power?  One allows the generator to warm up, the other doesn't.  Also, are your inverters in sell mode?  could we have the inverters attempting to "sell back" to the generator, and what would that cause?
 
The inverter should be able to be connected in parallel with the ATS, if you wanted the ATS to govern the excersize cycle, but the inverters can do the same thing with more flexibility. 
 
BTW, why a 12 volt system for a dual SW?  The thought of that much current flowing makes me wince.  Hope all the wire near your shunt is rated 90 degree Celcius or better.
----- Original Message -----
From: Travis Creswell, Ozark Solar
To: RE-wrenches@topica.com
Sent: Monday, February 05, 2001 9:55 AM
Subject: Generator Control- A Doozie [RE-wrenches]

I have a customer who already had a 22 kW kohler controlled by a automatic transfer switch.  We added solar and a dual SW inverter system to the house.  Due to the size of the existing generator and existing house wiring configuration I can't run the generator into AC2 on the SW's.  There are loads on the main panel that he would like to run still that shoudn't be ran of the inverters.
 
I am trying to figure out a way to prevent the generator from running when the grid is down and the batteries are charged while allowing the generator to start when (as) the batteries become depleted.  The customer is adamant about this being automatic. 
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