The service is 225 amps for the house. The generator/transfer switch are rated at 100 amps. Generator controlled circuit breakers will drop enough circuits in the house to keep the generator happy.
Maybe what you should do is place all the loads you want the generator to run during a blackout in a sub-panel, and place the transfer switch in the sub-panel feed coming from the main panel. The rest of the main panel would feed loads you don't mind dead during a blackout.
We were going to have 100 amp capacity in the pole barn, but we will be upgrading the service. The 100 amp panel will work fine as a sub-panel in the house for the generator loads. Instead of "generator" controlled circuit breakers, I should have used the phrase "remote controlled". SquareD makes a 24vdc operable circuit breaker. Try this link: http://ecatalog.squared.com/pubs/El...h-Circuit%20Panelboards/48840-496-04.pdf
They also make a handy power supply that snaps into the same sized hole as the breaker. The remote controlled breakers are very useful for load management purposes.