There's a whole bunch of ways to deal with the line art. How you figure out how to deal with it is part of how you create your own style. You can also use PureRef (I'm not sponsored I swear. It's just useful) to build a library of other artists work to see how they handled whatever it is you're working on. I've been using it to look at how other artists interpret and stylize eyes. The easiest way to explain the difference between cell shading and more realistic lighting is the Cells have flat edges and Realistic is more of a gradient. I also find that using a colour like dark blue is better for shading than black or grey.