The sading was done with the same tool as the lines, the pen tool in PaintTool Sai. Possibly not the same settings as default though.



To do this picture, I drew the initial sketch of RD on one layer, then on another layer drew her clothes. That way I can fiddle with the clothes easily without accidentally erasing any part of the body. Then on new layers I inked her whole body working like a sandwich, putting the parts that are furthest away under the others. So there's over eight layers on her head alone for just the lines.



Then the clothes lines.



Then I do the base colours on separate layers for each set of lines. The select tool and buck work great for this. This is around when I have to rearrange the layers to get the puzzle to work.



To do the shading I find the layer I want to shade over and select the base colour and open a new layer of it, and mask it. Using this method I can shade every part I want without going over into other areas.



Lastly the eyes are done again with multiple layers. For those I did the shading with the pen tool, a copic marker/watercolour tool and the blur tool.



I forget what I used for the clouds.

So tools, pen tool, copic/watercolour/, blur tool and eraser tool. That's it. Plus whatever the cloud one was.



Let me know if that helps any.