Secondary or "Sub" Categories
Secondary categories act as subcategories, but they can be searched directly without an associated main category. A product can be related to an unlimited number of secondary categories.
The Sort Order field allows you to "force" the order in which the secondary categories are sorted, rather than relying on alphabetical sorting. Secondary categories are first sorted by the numeric sort order, and then any categories that have the same sort order are sorted alphabetically.
Powerful Search Solution
The real power lies in the flexibility with which products can be searched. For example, customers can narrow or refine a search using secondary categories by searching for "Clothing" (category) and "Men's" (secondary category). In this way the secondary category acts like a traditional subcategory. But because there is no direct relationship between categories and secondary categories, customers can easily widen their search by searching for just "Men's" (secondary category only). The results will contain all products with a relationship to the Men's secondary category, regardless of what main category they are in, such as Shoes or Shirts.
Note: Relating Categories with Secondaries
You can choose to relate main categories with secondary categories using Store Settings > Display Settings. However, the relations are automatically determined at the product level. For example, if you create a product with "Clothing" as a main category, and "Men's" as a secondary, "Clothing" and "Men's" will now be related.