Hi, according to this page from Spine documentation:
http://esotericsoftware.com/spine-texture-packer#Folder-structure
you can export your images in different pages if you have them in different subfolders and if you have the "Combine subdirectories" option unchecked. But I haven't been able to do this from the export option.
The funny thing is that when I create the atlas from the Texture Packer option instead of the export option, it creates the pages according to the subfolders, even with the same options. It looks to me that is a bug, but I may have been doing something wrong.
I tried to run the export option to create just the json and the texture Packer to create the atlas and the images, but when I try to import to unity it's unable to find the regions that were in other pages. When I create both the json and the atlas+images, I can import them in unity withouth a problem.
I'm using Spine pro 3.4.02
I had posted this under the Editor threads but I think it belongs to bugs