When using the Warehouse feature, each product added to cart is internally separated by its own order and therefore having its own shipping. The customer won't see any difference when browsing, but will be presented with different shipping choices for each order during checkout. He will still make a lump sum payment. If the customer is only buying a single product or all products from the same warehouse, then there is no noticeable differences than a regular checkout.
The shipping method can take a custom rule. In the custom rule (XSL), you can query the warehouse information and decide on the amount to charge for shipping. If you're not familiar with XSL, you may engage us to write it for you.
Thank you