You can create categories in both Retail and eCom. 

• Create categories in Retail to keep the same category structure in both systems and to have automatic product-category syncing.
• Create categories in eCom to have separate categories from Retail. Manually add products to this category. 

Retail

Individually

1. In your Retail account click Inventory.
2. Click Categories, located at the bottom of the page under INVENTORY SETTINGS.
3. Click New category.
4. Type the category name and click Save changes.

The new Retail category will appear in the eCom back office under Products > Categories.

Import

You can create categories by import when adding items to a category. 

eCom

Creating categories in eCom can make it difficult to trace which categories have come from Retail. Since the product-category syncing will still continue for other categories synced from Retail, it's important to keep track of the categories that were created in eCom. Making a personal note including the category's original title and the reason it was created can help.

Read Creating categories for more information.