This is not available in the plugin. However, this could be easily done with a customization. I had tried out the interface with the ability to define multiple zones but unfortunately the page loaded too slowly.

The customization is actually quite easy, just open up MANUAL.pm and the function that calculates the total cost just returns a hash of "Shipping Method" => "Shipping Cost". (You can have multiple selectable shipping options such as "normal" or "expidited" ) All the values to do with the order are available so you'd only really need to create a rack of "ifs".