Hi, eBay stores and Auctiva store categories are quite different and at present cannot match.
1) eBay store: totally custom and can have sub-categories, this is available in your my eBay -> manage my shop.
2) Auctiva store: rather limited, can only be eBay listing categories not your eBay store categories. The feature to make custom search links to emulate eBay store categories in an Auctiva store is difficult to use and depends on unambiguous titles in your listings to make it work. I gave up after a while, and believe that custom eBay store categories will be supported in the future.
The import store categories is to make your custom eBay store categories available for use in listing creation so when the listings are posted to eBay they appear in the correct categories. Ok ?