really, just make one layer for lineart, and then another for color, and put the color layer under the lineart
and then color
also you know what that says for shading? The whole "use a black brush at low opacity" thing? NO
NOalso
never use dodge and burn, that's not how colors work, that's not how shading works
EDIT: how to color, the right way

see the 3 divisions of color at the top-left? The yellow/orange-yellow are warm colors, obviously, if you remember your color wheel
places where light hits objects get not only "closer" to white but also achieve a more yellow hue
so highlights = yellow
and of course you see the cooler blues and purples below the warm colors, and those are the cool colors
places where light is NOT hitting an object (at least, not as much as the highlights) are shadows, and those not only get "closer" to black but also generally more blue-purple
and below the cool colors are the neutrals, which are NOT COLORS, so DON'T USE THEM when you shade (and generally you should avoid them when coloring as well, because pure black/grey/white don't really naturally occur; some exceptions to the rule are using black in dynamic shading [where pure dark black is used for all shadows, kinda like Viewtiful Joe, No More Heroes, or Hellboy] and for lineart [like in my example])
if you want to see this kind of color theory in action just go outside in the evening, generally the whole "purple shadows yellow highlights" thing is strongly intensified then (especially in the clouds)
EDIT: also if you want some examples from artists with some actual talent (i.e. not me) then I can link some