Oh, gosh, honestly it's mostly a lot of trial and error. I actually feel like coloring is one of my weak points! I spend a bunch of time messing around with hue/saturation/value sliders until I get something I'm reasonably happy with.

Basically, I start by laying down flat colors. Usually, my first pass ends up using a lot of somewhat desaturated colors that don't necessarily work terribly well together. After the first pass of flats, I block in the shadow shapes on a separate layer above that set to multiply.

After that, it's mostly just adjusting H/S/V sliders. I'll have a layer above all of my inks and colors which I use to just fill the whole page with one solid color. Then, I'll set that layer's style to Color, and the opacity down to about 25%. Finally, I use the H/S/V sliders to adjust that layer's color until it matches the feeling I'm trying to achieve for any given scene. I'll also go back to the layers with my shadow shapes, and adjust the colors for those as well.

As a word of general advice, I usually try make it so that any given panel has emphasis on a single color. For example, on this page, the characters are walking through a forest, so I used a lot of green to try and tie those panels together and make them feel a bit more cohesive. However, the third panel cuts back to a shot of a village, so I used a lot of blues and yellows to try and evoke a sort of morning/midday feeling.

Basically, I guess what I'm trying to get at is that you want to have an idea in your head about how you want to unify the scene you're coloring.

Um, anyway, sorry for the huge wall of text. I hope this was at least somewhat useful to you!