Upstream or downstream breakers for sub panel
Often the stab rating of the circuit breaker mounting spaces are limited to less than the full rating of the busing, making it not possible to draw a single 200A circuit on the load side of the main breaker. I have seen combo meter panels that the meter feeds what is normal viewed as the load side of the main breaker and the stab connections feed the busing. Those panels usually have provisions for lugs at the top and bottom of the busing that could feed a transfer switch. 

The conductors feeding both panels on the load side of the switch would need to be sized at 200A unless the length of wire satisfied one of the tap rules. An alternative might be to change the panel closest to the switch to a 200A, feed it with 200A wire and take a 100A load off it to feed the remaining 100A panel.