There had been few queries on how to move files within the folders in a project. I would just write in words on how to do it. This applies to all versions of Atmel studio and AVR Studio 5.0 and 5.1.
From the Solution Explorer in Atmel studio, right click the file or folder that you would like to move. Then click "Cut". Then right click on the folder where you want to move and click "Paste". As simple as thatJ. If you want to move the file/folder to the root directory of the project then right click on the project and click "Paste".
Have a good time with studio.