We do a considerable amount of drop ship orders (about 1000/month) and the only way we know of to track the shipping cost is to add an expense line on each vendor bill for a "Other Charge for ReSale" which represents the shipping charges our vendor charges us.  Because we do not know the shipping charge amount until we receive the invoice in many cases, our finance department manually adds this chage expense line to every vendor bill. 

I would like to think we could have something similar to landed cost for drop ships where I could just have a shipping charge field that I can choose to populate.