pipeman,
Unforunately, you can't pick which auctions get appended with the store window and which ones do not. It's an all or nothing thing right now. Our old posting software did let you do this, so it's probably a feature we'll be adding down the road.
However, you can add/hide specific items from appearing in the store window. This page is actually really hard to find on our site right now, but we'll be fixing that shortly. For now, you can go directly to the edit items page here:
http://www.auctiva.com/stores/editstoreitems.aspxAs for your last question, each ebay Account can only be associated with 1 auctiva account.
-Kevin