The extension handles sending Shipment information between your Magento store and Shiptheory. But does not get involved with displaying delivery options and rates directly to customers. You can either use the built in Magento shipping methods, found in the configuration under System->Configuration->Sales->Shipping Methods. Or you can install a third party shipping rates extension such as this good free one: http://www.magentocommerce.com/magento-connect/webshopapps-matrixrate-1-multiple-table-rates-extension.html
Our extension is fully compatible with the built in Magento shipping method options as well as many third party extensions, including the one suggested above.
Once you setup frontend delivery options to customers, you can map them in Shiptheory directly to the couriers specific delivery methods.