BTW: The reason I wish to use Atmel Studio 6 is because it (should) give me more control over the microcontroller.
Relative to what?
And I wish to run a OS (preferably a RTOS) on it.
With only 2K of RAM? Why?
The same code, compiled by the toolchain in Atmel Studio 6 runs FASTER than the code compiled with Arduino IDE 0023.
Measured how?