I'm using custom shipping zones to calculate my shipping, we had negotiated rates from a shipping service for every product in catalog. We wanted to charge shipping cost for every product unit that is added to the cart.
Right now shopify calculates flat shipping fee despite of the quantity. The only work around I found is to add weight based shipping or price based shipping. Which is very difficult for us to implement.
We had about 20 products in our catalog and shipping price for each product is different, also it differs based on delivery zone. Setting manual shipping price is very difficult for us.