Projects have classification authorities that determine the appropriate levels of classification, and where necessary create separate compartments.

An important fact to realize is that the information security people making these decisions are read in to the full scope of the project in order to be able to do their jobs, but that doesn't mean they actually know all of the information within each compartment. Example: a weapon may have a compartment for the details of how the codes that authenticate a launch order are received and processed. Just because one helped make that compartment, and is even "read in" to that compartment, does not automagically grant them access to the contents of that compartment (the codes, in this case).

Some of the senior security folks in any classified project know the overall scope of the endeavor, and that in itself can be very significant (e.g. Manhattan Project, where the majority of workers didn't know what they were building). But that doesn't mean the classification authorities that create the classification guides to aid derivative classifiers necessarily know every detail of, say, the equations of state of plutonium. Their knowledge of the scope of a project and clearance to access each compartment doesn't mean they have access to all of the information within the project -- the need-to-know principle always applies.