I'm surprised nobody else has poked their head in here. There must be a couple of different routes for combining and I'm not sure how to help.
However, the combining I do isn't automated in any way -- meaning I don't have certain dollar amounts set up. I manually adjust the shipping charges myself on the final invoice I send out.
If you can't get a good answer here you might post at the eBay forums -- it's a good place for solutions to problems like these.