I use a Intuos5 to draw and usually draw completely in SAI, for some effects or sometimes for coloring I use Photoshop, though! I usually shade on a Layer Mask (Clipping Group in SAI) over the whole image in a nice color on multiply. Warm colors for warm feelings, cooler colors for cold feelings, usually I decide on a nice purple, for AJ a subtle red goes really well, tho! I’m not that good at explaining things, so have some pictures that explain how Masks and Multiply work:

The drawing with outlines and flats.

Shading layer above the whole drawing group. To prevent me from coloring over the area and into the background, I use the mask feature, which does that:

Shading confined in the right area. I do the same for highlights and everything else that isn’t an outline or a flat color.

If we set the shading layer to multiply, we turn that huge purple blob into a more purplish version of the color underlying it:

And voila, shading complete!
Sometimes I use different shading colors for different areas of the picture, but I think for most situations this method is easy and fast while still producing good results. I then smooth the shading out where it needs to be smoother, hard edges where something is casting a hard shadow, secondary light sources, reflections, etc. But that’s the basic method I start with.
I hope that was helpful!
Important: If you shade try to avoid any color involving grey (or even straight black). For highlights also try to avoid straight white. Be creative with your colors! Be bold! I’m nowhere near as bold with my colors as I should be, I’m trying, tho!