While you can print up to five labels per sale, the shipping calculator does not know how to handle multiple boxes. The best you can do is use an equivalent weight, which will generate close to the correct shipping amount.
First get a quote for each box going between your Zip Code and some arbitrary Zip Code at least Zone 5 from you, and total the amounts. Make sure you enter accurate weight and dimensions.
http://www.ebay.com/shp/Calculator
Then quote a single box between the same two Zip Codes and increase the weight until the cost is the same as the previous multiple box total. Now use this weight in the listing.
Note, that if the total weight goes over the maximum allowed, this will not work. Then you will have to use a different approach.
