Learn to do other things with your lines so you can get rid of them. Right now you use them to divide sections of you art so it shows shapes.
On a side with shadows it is fine for the lines to be black, because that side is shaded anyway. When there is a side light only hitting on side of the shape it is better if it is the color of that light. If you take out lines then you need to replace them with light and shaded areas.
It looks like your art is heading away from lines, so at some time you might want to start drawing silhouettes and drawing details or draw details until they show you where the edges are. Both ways work, but the second way would be quicker.
Something about the way I'm coloring leaves gaps where the lines are. Most of the time I select areas to erase/color respectively, since I don't have a steady hand to get smooth edge, but it seems like no matter how I select, there's always things missing. Shading, highlights, occasionally the base color. This probably has more to do with me, as an artist, than the program, but there you go.
well if you have the line art about the layer you are coloring in you could just be coloring it in like a coloring book, staying in the lines. You might want to change the opacity of the actually lineart layer itself that way you can see through it