Hi Joe,
Yes, all active listings, including eBay store items, can potentially be placed in the store window.
However, the only way you can control what goes in your store window is by making items hidden. To do this, go to Auctiva -> Store(tab) -> Edit Items. Items that are made hidden will not be shown in your store window the next time it refreshes, which it does about every 2 hours.
-Mike