Think of the H&E stain as a triage stain. It is used as an initial screening. It gives an overview of the structure of the tissue being examined and enables these structures to be differentiated from one another. From this, the pathologist can determine if the tissue is normal or pathological.
Often, a diagnosis can be made based on the H&E alone. However, after reviewing the H&E slides, special staining may be necessary to make a more specific diagnosis.