To paint from one layer to another using the clone tool do the following ;
1. Set the clone tool to aligned and current layer
2. In the layers panel click on the layer you want to sample from
3. Set your brush size and Alt click anywhere on the image
4. In the layers panel switch to the layer you want to clone to
5. In the clone source panel type 0 into both the x offset and y offset boxes (do this even if they say "0" already)
6. Brush onto image - the brush will be aligned to the layer below
An alternative method is to paint with the history brush.
1. Set your original image as the source in the history panel
2. Paint onto the new layer in the image with the history brush tool
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Some of my edits have eaten into the illustration itself and since I used some destructive edits, I can't just play with a mask.
If you have the (imperfect) cut-out on a separate layer, above the full image, I'd just use that to make a mask, and go from there.
- Duplicate the base layer.
- Ctrl-click the cutout layer to load it as a selection.
- Target the duplicate layer, and click the layer mask icon. This automatically loads an active selection as a layer mask.
- Delete the cutout layer, you don't need it anymore. Now you can just work on the mask, and paint back if you overdo.
Thank you both. I don't know how to set two answers as correct, but let me know idf there is a way. Great methods. I really appreciate the help.