Do you want to do the whole SD/HD atlas swap? If so then yes, work with a fixed size root, and create 3 atlases. First atlas is your SD atlas. Second atlas is your HD atlas. Sprite names in both atlases must match. The last atlas is your Reference atlas. Set it to point to either HD or SD. If SD has pixel size of 1, then HD needs to have a pixel size of 0.5, and sprites inside it need to be exactly twice the width and height of your SD atlas. There are plenty of topics on the matter in the forum, including an atlas swapping script.