Since you are selling on ebay you are using their checkout (even if it doesn't seem that way). I was having the same situation as you...Here's what worked:
First go into ebay and use bulk edit to add a combined shipping rate to all your listings (it was way easier than I expected it to be)
Then go into your Auctiva listings under the shipping tab you will now have an option to check that will add your ebay combined shipping rules to your listing.
So NOW when someone buys more than one item they will automatically get combined shipping.
I always required immediate payment with my Buy it Now listings, but I have heard in some categories ebay is actually adding that themselves, even if the seller didn't want it. I have had no problems using the combined shipping, but you HAVE to change everything in ebay first or you won't have an option in Auctiva.