A custom category is a category which you have defined yourself (in contrast to one defined in InfoSum's Global Schema).
Custom categories are defined separately for each dataset. When you use your bunker to assign columns to categories, you have the option of defining custom categories (instead of, or as well as, using the ones available in the Global Schema).
When you define a custom category, you give it a name. Two custom categories in different datasets will be matched together if they have the same name. So, if you use custom categories, you may need to coordinate with the owners of other datasets to ensure that you all use the same name for the same category.