auctiva store and ebay store are two different animals.
simply put, auctiva store is merely a page of your items for sale on ebay. then there's the store 'window' which is the gallery that is inside your item's description and has pics of your other items for sale.
for an example of the store window - see http://cgi.ebay.com/Landstroms-Black-Hills-Gold-Mens-14...Z92845QQcmdZViewItem
Since you have an ebay store, you want to import your store categories. click the My Account tab, then in the left column on the page click "eBay Settings" on that page you can import your custom store categories from ebay. (you'll need this done before you create listings if you want to put your listing in your custom store categories) shortcut to that page is http://www.auctiva.com/account/ebayaccount.aspx
back to auctiva store topic - your auctiva store will automatically be populated with your ebay items that are up for sale. (regardless of whether you have the store window turned on or off).
Your auctiva store window - turning it on causes it to automatically be inserted in all your active ebay listings and automatically added to any new listings (whether you launch them from here, ebay, or another site). Turning it off does not remove it from listings nor does it keep it from automatically adding new items to your store window. Turning it off only prevents it from automatically being inserted into listings.
hope that helps