We are currently unable to accommodate combined invoices. We will be adding this feature for our phase II release later this year. Until then, there are a couple viable options:
1) Enable the "Allow Buyer to Edit Total Amount" feature in your checkout settings. This will allow the buyer to edit the checkout in order to reflect reduced shipping costs or multiple items.
2) If you turn off Auctiva checkout, customers will revert back to the standard eBay checkout for your newly listed items, which will allow you to combine invoices. Auctiva checkout can be disabled at Auctiva -> My Account(tab) -> Checkout Settings.
However, listing that were posted via Auctiva when Auctiva checkout was enabled will still go through Auctiva checkout.
I'll post to this thread when I have more info about the shipping discount issue.