The current rating of an ATS refers to the maximum current it can carry through its contacts in any direction. If the main service is 100 amps, you're okay. If it's 150 or 200, you need a 200-amp ATS.
This has nothing to do with the rating of the generator's breaker; that's there to protect the generator from overload. If you attempt to use more current than the generator can produce, its breaker will trip.
