As an update for anyone looking at this..
I managed to get the raspberry pi build going. It seems after running
source oe-init-build-env rpi-build
the local.conf from meta-atmel was copied into the rpi-build folder. This local.conf amongst other things had
DISTRO ?= "poky-atmel"
Which was causing the issue.
However if anyone could point out best practice on folder location I'd be grateful. Build folders inside or outside the poky directory?
Regards,
Owen