As for the best ways to setup your shipping I don't have much advice for you since it will all depend on your needs for your packaging ect. Perhaps some others here could give some pointers on the way they like to have it setup for them.
For the amount eCart does interact with the FedEx API to get the shipping value. This quote is then used as the shipping charge in the cart. This is all done automatically for you. If you would like to adjust the shipping charge you can do so in the cart object by going to the shipping tab and editing the rule.