Man, it's hard to remember the Daily Doodles when I'm working on stuff! This is a much more realized before & after of my latest Angela's Magic Lesson epilogue. You can see the slight changes made from the original pencil drawing to the final cropped and colored image. Almost all of the color is done by colorizing entire layers and erasing the stuff I don't need. A blue layer is on top of a yellow layer, so I just needed to erase the moon, windows, and Shelley's eye. I actually copy/pasted the bite on her arm and colorized that too. Finally, I put a radial gradient on top to darken the edges and hopefully draw your eye to the characters' faces.
I doubt this is a groundbreaking method in any way, but It's a method that suits these drawings well. It preserves all my penciling, and I just think it's interesting to use the eraser as my primary tool, rather that just a corrective one.