You need to decide how to split your products into shipping groups. Usually the product type or category is a good guide. In terms of shipping the highest price of the products in the cart from a specific group will be used, plus half the price of subsequent products in the same group.
To setup shipping groups go to the Attribute Management under Catalog. Then find the attribute “shipping_group”. In Manage Label/Options add each of the shipping groups. In the example below we have BOOKS and DVDs. Products will then be assigned to either of these.