Hi makeupmystique,
1) If you list through Auctiva, the store window will automatically be displayed at the top of each listing. The only reason it appears at the bottom of imported listings is because it is appended to the active listings.
2) The store window will automatically be inserted into store listings as well. It generally takes 4-6 hours from token generation for all your listings to be imported and appended with the store window.
-Mike