Here's an animation showing how I finished up the pencil drawing for the first page of The Rough Pearl.
First we see the "raw scan" of the drawing, then we see it once contrast has been added, followed by some "dodging" and "burning" to clean up graphite smears in some areas and punch up lines and shadows in others. I never use the actual "Dodge" and "Burn" tools in Photoshop - I use color correction Curve Layers (one with the midtones pulled up to brighten, one with the midtones pulled down to darken) controlled by Layer Masks.
Next I manipulate the drawing to fix compositional and proportion problems. I always flip the page (Image Rotation > Flip Canvas Horizontal) as this helps me spot the areas that need fixing, then I usually use the Liquify filter to smoosh the areas around until I'm happy with them. Sometimes, as in the case of the woman's face on the computer monitor in panel one, I select individual areas and resize them with the Transform command. I also frequently draw in new details in Photoshop - for example, in panel three I needed to extend the image to replace a thought balloon I took out after deciding it made Adam sound too angry and misogynistic (he's only slightly angry and misogynistic).
Finally, I add color and refined lettering. The color is on a Layer set to Multiply and is controlled by a Layer Mask where I brush certain areas out to lighten and emphasize them.