I don’t think that Atmel Studio has any methods of creating interrupts, but it does include lots and lots of drivers that already have interrupts service routines defined in them. If you are using the FreeRTOS peripheral control drivers that are part of the ASF then you don’t need to write the interrupt service routines as the code manages the interrupts and the DMA for you. See http://www.atmel.com/images/doc42049.pdf
If you are just wanting to write a FreeRTOS compatible interrupt, then read the “Interrupt Service Routines” section of the web page that documents the demo you are using. Also if you are using a SAM3 or SAM4 part ensure to follow the rules regarding interrupt priority configuration very carefully – that is documented on the same page.