Hi,
Straightforward solution is to create separate page template for each section. But, this could be a pain.
Second option I see right now is to play with
visual inheritance and with page place holders. The idea is that you will add another layer of pages, "submaster pages" for each category. These won't be displayed on the live site, they will just hold the page template with the advertising zones and page placeholder in which the category and its sub-documents will be displayed.
For example:
-Sports (page template with ads zone)
--Sports
-----articles
-Science(page template with ads zone)
--Science
-----articles
Best regards,
Juraj Ondrus