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