Download Manager Pro uses custom categories and tags similar to post categories and tags. Categories may be setup in a hierarchy and show up in the end user interface for searching and filtering. Tags are not hierarchical and are best used to display a list of a group of documents from multiple categories.
Document categories are added under the Documents/Categories menu in the WordPress Administrative Dashboard. To set up a hierarchy, add the parent category first and then add new categories under the parent. If you plan to have different categories on separate search pages, for example: Category A with sub-categories a-1, a-2, etc. and Category B with sub-categories b-1, b-2 and allow users to search only Category A or Category B without seeing the other category, then set each up as a hierarchy so that the parent category can be placed on a search page.