I think it would be better to use the unmodified versions of FreeRTOS or ChibiOS with Atmel Studio. Both of theses systems have AVR ports and examples.
I know FreeRTOS and Atmel are cooperating to make their products work together.
I really like ChibiOS/RT on Due. It is fast, takes a bit less memory than FreeRTOS but has more features.
Nill RTOS is great when you need minimal memory use and simple features are adequate.
Nil RTOS is experimental and not really supported yet by the author. I am personally supporting Nill RTOS mods for the Arduino core.
I assume you are not using the Arduino core software. My mods were to allow use of an RTOS with the Arduino core and Arduino libraries.