Setting up the shipping for your store is an important and sometimes complicated process. You have a variety of options in how to handle the shipping calculations for your store, and with a little custom coding, you can come up with even more possibilities. There are two main classifications of shipping types: custom shipping types in which you configure how the amounts will be calculated and automated methods that rely on external shipping APIs to calculate the shipping.
Version 6.50 now includes the ability to use multiple shipping types, along side each other. Please note that you can still only use one custom shipping method at a time, as those all use the same database table to hold their shipping rates. Of course, if you really want to use more than one of these, you can always custom code the store to do so (typically the only reason to do this would be to use a different shipping method for different products, which itself requires custom coding).