Your user id and the Store name do not necessarily have to be the same thing. eBay will allow your particular User id to have a different Store name. So if your User id is "Sweetcakes" your eBay store could be "Sweet Things" by sweetcakes.
The auction profile in AW2000 can have whatever name you want it to have. It is the User id which must be correct.
Some sellers set up stores with a Store name which isn't the same as their User Id. And others use their User Id. It depends on your approach to marketing your Auctions. I susbscribe to the school of thought which uses the same user id for both regular auctions and eBay store. But I have friends who do it the other way.
A separate Auction profile for eBay stores in AW2000 is a must. As when you create Auction lots, you must select if the Inventory Item will be a regular auction listing or an eBay store listing.