For me I like to set up layers like an animation cell going with lineart and then making a base for each color, it was tough at first but once you get used to it it saves soo much time, but there is nothing wrong with painting everything on the same layer. Anyway, as for the painting itself try starting off with values before color or at least using black and white to show the contrast and where the light is from and hitting and try to make it consistant throught the painting, try to set your drawing in a way that you can easily identify with the orders of light. For me for example I like setting up my main light first, then my secondary, then bounced light.
Im also still learning so I hope this helps if even a little. 
