Once you have changed the order of your categories on eBay -> Manage My Shop. You will need to update the category settings in the Frooition Software.
Click 'eBay tab'.
Select your 'Storefront' from the resulting sub-menu.
- This could be Branded Storefront, Signature Storefront or just Storefront depending on your account subscription.
Navigate to the 'Category Manager' section.
- This could be labeled as 'eBay Store Cats'.
Once here, you will need to select 'Update Categories from eBay'.
The final step is 'Save Categories'.