I have the same problem but solved by exporting several objects as .obj and open the file in Deep paint. Paint it until you are satisfied, then export it to photoshop and every channels(bump, diffuse, specular map etc) will be automatically divided into layers. Then you can do some further edits if you want....
Important, you have to lay out UVs if you want to paint polygon objects.
Hope you understand what i mean.
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