Make sure you have your feeds setup the way you want before mapping categories.

The Categories tab allows you to build a custom category tree for your site. At first this may seem like a lot of work. But it provides you with the opportunity to create a unique category tree which will help your site rank much better among your competitors.

The New category button lets you create a new category. Specify a Name and optional Parent and Description and click Save. The Description is displayed to visitors when they click the category. Use this field to help your site rank better in search engines by providing unique content per category. After creating a number of categories, using the Parent option to build a tree, you should then map your categories to the imported products.

Click Map product categories to open the mapping screen. This screen will show a list with all the categories and subcategories imported from your products database. Behind every product category is a list box with your freshly created categories. Now simply select a mapped category for each product category. You may choose to only map product categories, ignoring subcategories. In such a case when a visitor clicks a mapped category all products from both the product category and all underlying subcategories are displayed.

Sort categories sorts the entire tree alphabetically. Parent / child relations are not changed when sorting.

Don't forget to Save.