Are you using Auctiva checkout or Ebay checkout?? I only use ebay checkout because I have heard of too many people having problems with combined shiping.
Either way...first you have to set your 'rules' in ebay preferences. Then in Auctiva (if you're using their checkout) you will see Combined Shipping Discounts with a box to check to apply your Ebay rule. (be sure to maximize the shipping section)
I don't use it so I can't be sure but I would think that this is the way you would do it.
If it's wrong and doesn't work, you can always invoice directly through Paypal.