Here's a progress of how I typically do color.
Under Painting
Do background colors first, so that you can maintain a good color balance throughout.
Flat Colors
The reason I flat against the background color is this:
Colors appear to the eye different against different colors, it's a weird thing your brain does.
Add Reflections from Surrounding Environment
Light will bounce off objects and the colors will mingle.
Start with Cell Shading
because my comic is manga style, I cell shade the illustration using a light blue set to multiply layer. Adjust hue/darkness where needed.
More Shading
Smooth out the edges of certain shapes and textures using blending brush (watercolor is good). Gradiant overlays on the shadow layer for more depth.
Highlight
Add shinies where the light hits objects with varying softness/glare.
Over Line Art Details
On top layer, sharpen lines where needed or draw highlights over lines to enhance lighting effects. Color lines where softness is desired using overlay layer. Draw stray hairs, grass, sparkly dots, etc.