if the ceilings and floors need to be repaired (check box field), but the roof does not, the third layout would be generated with only the ceiling and floor fields (quantity, cost), not the roof fields, or any of the other myriad building systems fields.
Where you have fields in the above quoted statement, think records in a related table. This does not require you to use a different format on your report and data entry layouts, but does require a significant redesign of your underlying data model. By having a related record for each "check box", records where you have recorded such a check box will exist and records where you have not made such a selection simply won't exist and you can set up a report on the resulting found set of "problem area" records.
I was trying to get around having 200+ records associated with each building and have the basic file structure be database per school district (or client), record per building, associated fields per question/category on the state form (state form is one per building). the thinking is that this makes data entry easier in the field, rather than have to create new records for each question/category of building system. Picture shows a page of the state form. Either the building is the data base and each question is a record with fields, or the client is the data base and the building is a record with fields?