To setup real time shipping calculation:
Go to General Settings -> Shipping Options ->
DISABLE SHIPPING - uncheck
Enable real-time shipping calculation - check
you will have to register with shipping companies before you can use real time calculation:
USPS: Open an account at http://www.uspswebtools.com/
and enter your username and password on this page:
FedEx: Enter your FedEx account number of that page:
UPS: Enable "UPS OnLine Tools" in "Modules" menu;
go to "UPS OnLine Tools" menu: http://www.yourdomain.com/store/admin/ups.php
and click [Register]
Go to "Shipping methods", disable all methods and enable only methods you want to use.
Test the shipping in the test menu and in the cart.
Note: you will need the weight setup for all the products for correct rates.
Let us know if you need help with anything.