To correctly handle downscaling, each image has to be downscaled (right now, you have to do this manually) but we will be making it so you can downscale automatically in the toolkit in a future version. You can't downscale the atlases, as that would incorrectly merge pixels that shouldn't be merged. We supported manually downscaling first, as that produces the highest quality results, as photoshop downscale filters are far nicer than the ones built in to Unity, and you can also tweak them manually for better quality.
If you want a cheap and dirty solution to this right now, enable mipmaps and use QualitySettings to switch to a lower resolution for your other platforms. You can find some samples of how to do this on Unity Answers, but that seems to be down right now.