To have the maximum of control, this needs to be done manually. Nonetheless, If you have a look at the AppKernel.php of the Terrific Composer, all of the Modules – each of which is a separate Symfony2 bundle – are registered automatically by looping through the /src/Terrific/Module folder.
This is possible, because all of the Modules share the same namespace. But for all other bundles I strongly recommend you to register them manually in AppKernel.php. As most of the 3rd party bundles need some configuration, there are some manual steps anyway.