You use named user channels as inputs for handpainted masks There's sod all documentation on the Allegorithmic site but Bradford Smith put up a video about using them on paragon a while back. It's pretty straightforward, you'll work it out.
I made a tutorial in Youtube on how to make custom substances with exposed params. I hope this would be helpful for some, perhaps new users of Substance Designer and Painter. It's pretty great we can expose image inputs so we can use things like Position maps, curvature maps and World Space Normal maps with our substances…