Starting to color
My coloring is almost as much process as art. I've got a panel template with approximate lettering area roughed in with guides. It's 600 DPI and has five channels built in, the normal CMYK ones as well as a PUREBLACK that allows me to have an action select a layer and turn it into lineart in my printer's rich black with a transparent background. I've also got actions for an Expanded Fill (which expands the selected area by two pixels to make the color trap underneath the line art) and a Contracted Fill (which does the opposite, and is useful when I have a character selected and need to make the area below him white).
I've also got a pallet of LNC colors. Once a character is colored, those characters remain pretty fixed. So, the Crusader's uniform is always the same color, Abby's hair is the same shade of yellow, etc. The less I need to think about that, the faster I can go.
I use a Wacom Intuos 3 tablet to color with as well. I couldn't color without it.
Panel Two start
I'm going to focus on the second panel, because it's the most typical. I've taken the images from my master scan, resized them and placed them where I need to. I always try to make sure the art is loose enough on the edges to be moved around where needed. And I try to leave lots of space up top for lettering.
Backgrounds
I also add in the background elements before coloring the main characters. I did the back wall of the Airblade in a separate window and save this to my library so I can reuse it when I need to.
I've also now inked and colored the seats so that I can cut and paste them down. The seats are done without shadows so that I can add them where I need to on the final art.
With the characters, I select the white areas around them with the magic 
wand and delete that. Then I select the ink layer, change it to Darken, make a new folder and put in a layer that I Contracted Fill with white. It's good to have this cardboard cutout layer, so to speak, because it's then easy to select and add in the cut color shadows which I'll do afterwards. More on that in a minute.
Coloring the characters
I go through, selecting all the areas I can and fill them with color. Darkblade's easy, because his colors are in my pallet. Charlotte's outfit is not in that list, so I have to either create it or duplicate it from a previous panel. So scenes with civilians always seem to take longer.
I'll run as many layers as I need, but colors will share layers. If lines don't connect and I have to select and color an area by hand, I'll draw it out in the color I want it and Expanded Fill the area. If it's something like Darkblade's mask, I'll color the burgandy area and then, on the layer below, sloppily add the yellow eyes. It's easier than trying to do the same precision fill for the eyes, and helps with trapping.
Ladies' eyes, like Charlotte's, though, are always on a separate layer. Next, I'll add a shading layer, and one of the "rules" of the book is that eyes don't get shaded. I tried it once and didn't like it.
Shading
I make a shading layer right below the female eyes layer. I set it to multiply with an opacity of 30%. Then I select a shadow color. I have a dark brown for daytime scenes, and a dark blue that I sometimes use for cooler night scenes. Then I select that white fill layer that covers the characters and 
start drawing the shadow. I then deselect the layer so I can draw outside of the character area and extend the shadows off of the characters.
Lastly, I select the black line layer and select my Blacklineification action (and yes, that's what it's called.) It creates a white layer underneath the black line and merges them (fixing any "holes" in the black line layer), cut it out, pastes it to the PUREBLACK channel, selects it so that the black lines are selected, and goes to the original layer and fills it with the richblack color. It then renames the layer so that I can use the action on multiple layers without problems. Sometimes I've got characters on multiple layers, and each black line is rendered separately.
Last Tweak
Since they're flying in the Airblade, I wanted an establishing shot to show them inside. I wanted to shoot through the window so you can see them inside, and add a little cockpit control area for Darkblade. I've got a window set from the first appearance of the Airblade. So I dropped that on top, too.
Done!
Then I save two versions, a fully layered Photoshop file, and a flattened one. The layer version is so I can make changes if I need to, and the flat version is for placing in the lettering file. Flat files are smaller.