This is the major distinction between Categories and Series/Sections. Only a single choice per submission is possible for Series/Sections, but multiple Categories can be chosen per submission. I think Categories are a better choice for subject areas.
While we don’t prescribe a specific single use for Series/Sections, it’s probably best to use it to capture an administrative distinction, like the type of submission for workflow purposes (research, review article, etc) or even administrative unit (e.g. which lab among several that co-publish might have undertaken the work).
Public Knowledge Project Team