You can change the sort order for product categories and other content in bulk via csv import by using the following columns:
Content type (eg. Product Category or Blog, etc)
import/export > import wizard > inventory import
Follow the prompts
The higher the value entered, the higher up in the list an item will appear. The sort order field is therefore often referred to as the "priority" field. For example, 99 will appear above 89. This gives you the flexibility to add a new category at a later date and have it appear at the top of your list without having to reorder your entire list.