Hi Mia,
I can help answer a few of your questions..
Unfortunately to remove the store window from your active listings you will have to go in and revise each one on eBay and delete everything between the <!--ASW--> tags.
You can customize the location of the store window in future listings by inserting the HTML for it yourself into your auction descriptions by clicking on Store Window from the Store tab, then Store Window HTML.
Or, you can just choose a different style of store window and have it automatically positioned for you. The Horizontal scrolling window is set to appear at the top of your listing, while the Vertical window will appear on the side and the Full window will appear at the bottom. You can choose a new store window style by clicking on the Store tab, then Edit Store Window.
You can 'categorize' the items in your Auctiva store by creating custom searches. Custom searches will provide a set of links down the side of your store for each category just like your eBay store does. You can do this by clicking on the Store tab -> Customize Store Window -> Select/Edit Style -> Custom Searches.
You can group your listings together on Auctiva by using Folders. So you can create a folder for jeans, another for jackets, etc, and even color code them. To create a folder for your listings click on the Listings tab, then the Manage link in the Folders section. Then when you are creating a listing, be sure to select which folder you want it to belong to!
Let me know if you have any more questions!
-- Auctiva David