I think you should stick to this style, the dark lines stand out and the whole thing is pleasing to the eye. Is there any particular method you use for the outline-less parts or is it just done like normal?
First i make the lines, and make a copy of that layer. Then I put color on the lower layer. When I have all the colors in place, I make all the black lines transparent. And I expand the colors so they fill where the black was. Then I can erase the lines as I want in the top layer. Then there is some fixing of some details to do.