You need to create an eBay store Auction profile in Aw2000. Then when creating an Auction lot, you elect whether you want the item to go to the regular eBay auction or to the eBay store.
Go to File | Auction Profiles. In the Auction site field, select eBay store as the value.
The Auction Site user id is your user id, not the eBay store name. Complete all the fields just like you did for your regular eBay Auction profile as the fields apply to your eBay store.
After you create the eBay store Auction profile, when an auction lot status is "Offline, Never listed, Hold, you can change the Auction profile by selecting the drop down. OR you can highlight records in the Grid View, right click and select "Change Auction Profile to".
Does that help?