You mush have both AVRStudio and WinAVR installed.
Create a new project, Project -> Project Wizard, on the next window click on "New Project", then on the next window click "AVR GCC" under the Project type. This tells AVRStudio that your project uses a C compiler.
If you are already working on a project file (ie it was previously created) get the project's Project Options (Project -> Configuration Options). Goto "Custom Options" check on the "Use WinAVR" check box in External Tools if its not checked.
Hope this helps you out a bit.