If you are only looking to provide power to certain circuits then you will need to add another panel. This EM panel would receive power from the transfer switch. The transfer switch would receive Normal power from either the 400a or the 200a panel and EM power from the generator.

If you power the 200a panel from the tranfer switch then the entire panel would be 'hot'. If the combined load of the 200a panel exceeds the capacity of the genset then the C/B in the genset will trip.