Anything in the Resources folder is included in the build, but not loaded until you load it specifically.
If you want something to use an SD atlas for low res iphone, HD atlas for iphone retina and ipad, while keeping everything pixel perfect (smaller on iphone retina than ipad) then make a little script that sets the UIRoot manual height different on the ipad. If SD atlas has a pixel size of 1 and HD has a pixel size of 0.5f, you set your root manual height to half the height of the highres device - that is, the same as SD iphone for HD iphone, and actual resolution height /2 for ipad (either 384 or 512).