Hi.
Sorry for extremely late reply.
I am glad you like the program :)
Regarding your problem with black textures it's because when you export a model from Blender you need to enable tangents in the export settings. I've mentioned it in the help section of AtlasMaker. I struggled for the longest time trying to figure out why my textures got black in parts. :)
In next update atlas name, width and depth will be in the json. Thanks for the suggestion!
There will also be a lot of other improvements and changes in the next update which should be up there in the next couple days.
zooperdan