If you are feeding the 200A panel from another panel with a 100A breaker, then the 200A breaker in the second panel is only acting as a disconnect and does not need to be removed.
If you are feeding the 200A panel directly from the meter with a 100A service, then you need the 100A breaker in the 200A panel...
I used a 200A panel at my place with a 100A service; I used a 100A breaker to backfeed the panel (with a retention kit) and I just pulled out the 200A breaker to save for when/if I upgrade to a 200A service.
The cover in my panel came with the knockout in place for the main breaker, so I just never removed it.
Edit: you really should probably start another thread at this point...