Hi, I just opened up an auctiva account and listed some items just a few hours ago. I'm confused about how I can setup my eBay shipping discounts and combining invoices and have that sync with the auctiva checkout.

On the auctiva profiles its fairly simple and straight forward for shipping. Put in the price for the flat rate + any additional item and voila you're done. But it seems to be more confusing on eBay. Can anyone please give me a detailed instruction on how I can add a rate for additional items for combining invoices?

Yeah, eBay's combined shipping preferences are a little confusing, and they like to change things periodically. If you're comfortable listing with Auctiva and plan to list all your items from here, the profiles should work just great if you're selling more than one of the SAME item. But it's not necessarily "combined shipping". Combined invoices involve purchases from one buyer of multiple items (with different item IDs) from the same seller. For those, you may need the combined shipping options set up in eBay.

Have you seen this page?
http://pages.ebay.com/help/sell/shipping_discounts.html

Once you have your settings set, you'll need to check the "Apply my eBay promotional shipping rule" checkbox in all your listings (or your shipping profile).