Hi. From what it sounds like, you've scheduled from Auctiva through your 'saved' listings? If so, yes you'll need to end your store listings.
If you scheduled them via eBay, then you won't need to end them from your store. However, you will be charged for the scheduling.
What I do is go through the eBay bulk list thing. You can check all you want to go to auction from your store, edit the start price (mine defaults to .99
) and send them to auction. This deletes them from your store inventory at the same time. Of course that's only going to be useful if you can be at your computer when you want them to be moved.
Is this what you were asking?