Defining categories is a general option as part of the Admin settings. Sites and all their links/pages may be allocated to one or even more categories.
Including/excluding links from being indexed by the "URL must (not) include" options is working site specific and needs to be defined individual for each site URL and will of course separate single pages of the site from being not indexed. This option is working independent from the category definition. It is a sub-setting of your category definition, as each site URL may contain different "URL must (not) include" directives.
Please keep in mind that the user of your search engine may only select "categories" in the advanced search options. In other words, your "URL must (not) include" settings will be invisible and not recognizable for the user.
Following your above example, you will have to allocate your (one) site to both categories and separate the according pages by means of the "URL must (not) include" definitions.
Tec
