Currently AVR Studio 5.0 doesn't allow you to add all the files under a folder recursively to the project in a single shot. However this will be supported in the future but until then this small little extension might be helpful for those who actually want to do it. To start, please download the extension from here.
To make it work.
Close AVRStudio 5.0 and double click the downloaded file. It will install the extension to AVR Studio 5.0.
Launch AVR Studio 5.0 and open/create a project.
Copy the folder (that contains all the files you want to add) under the project directory. Currently this extension doesn't support adding a folder external to the project directory.
From AVRStudio 5.0 select , Tools Menu -> "Add Files to Project".
Select the folder, and click Ok.
Now you should see all the files under your project menu :)