If you need to assign a product to a several categories (sub-categories, parent categories, root category), you can use few approaches to achieve it:
1. If you need apply assign products to list of different categories, you can just select "Categories IDs" column in extension settings sections. Then you can edit values for "Categories IDs" column with different list of categories for required products. You can specify Categories IDs with comma separator. It can be different stack of categories for different products. Then click "Save Change" to save all changes.
2. If you would like to assign products to same list of categories you should use "Add Category" mass product action, which you can find in dropdown of mass products actions. This mass action is sensitive to extension setting "Category Names/IDs" - if "Category IDs" is selected, then mass action will expecting list of categories IDs with comma separator, otherwise it will propose you to select one category from tree of categories available in your Magento store. You can navigate to full extension settings page by clicking "Detailed configuration .." in settings section of the product grid page, or you can go to System > Configuration > IKSANIKA > Advanced Products Manager > Mass Actions Settings > Categories Name/IDs > Category IDs.