Since this is a residence, and there is a single main service for the home, one transfer switch for the main disconnect would be the choice.
Is there some reason for attempting to connect 2 ATS switches
as opposed to one?
Size of one is too large maybe?
Maybe I am missing something?
Having 2 panels activate the generator, is counter productive, since they both receive power from the same main feed.
If one goes out, so does the other.
Are you installing some time of safety net, like load shedding to one of the panels?
Running the 2 panels, you can overload the generator extremely quickly and it will never even come online.
How are the panels connected to the service?
One main disconnect?
Each panel from the meter base with no outside main?