Ah, much better. Now that's the Nina and Jess we remember.

Back in Photoshop, a layer is added above the artwork, called S+H (Shading and Highlights). Everything here is pure black and white, but looks the way it does because the opacity is turned down to 35%. Originally, the shading was only 20% opacity!
This process takes roughly an hour or so, but makes the comic infinitely more pleasant to look at. There's no real rules to follow in this step, I just use my best judgement on where to place shadows.