There is a free add-on for Blender - ucupaint 1.1
It allows Blender to behave like a multi-layer paint program
Download:
https://github.com/ucupumar/ucupaint/releases
Tutorials:
https://www.youtube.com/watch?v=LtZTLWdQOVI
https://www.youtube.com/watch?v=u513zWrU86E