Doxygen Integrator gives you an option to generate the documentation as a part of build. For that purpose you should check the checkbox "Generate the documentation as a part of build?" in Document Generator, and use "Save Settings" button to save the settings. If your build suceeds you can generate the documentation automatically. The warnings/Erros will be shown in the ErrorList pane of Atmel Studio. Double clicking on error/warning will navigate you to that pericular line, which has errror/warning.
