After that, it's time to color (which begins at around 53-54 minutes into the video)! I tend to "cheat" a little bit when using this style, because the clean lines lend very easily to using a magic wand/fill method. So, step 1 is to create a new layer underneath your lines. Afterward, go back to your line layer, select the magic wand tool and click outside the line art. This is to make sure you are getting all of your subject as well as underneath the lines. Be sure to select any spaces that might be missed, such as between legs or if a tail or limb circles around and cuts off your magic wand. This means there will be less cleaning up later.
Next, you'll want to go up to Select > Inverse to switch your selection from the area around your subject to the subject itself. After this, you'll want to go to Select > Modify > Contract and choose a pixel value. This can depend on the size of the image you're working on, but I tend to work at 6400 pixels across, so my contract pixel value is generally around 5 to 10. What this does is prevent the icky, pixelated halo that can appear around your lines by removing those pixels from the selection.
But, you might be wondering, what about if you want your color layer to be neatly underneath your lines? Don't fret! Just have your line layer select and then go to Select > Load Selection and be sure to check the "add to selection" box before hitting OK. This only works if your lines are on their own layer, so if you started with traditional media or have your lines on a layer with a white background, you'll have to take a few more steps to get rid of the background on that. More on that involved process at a later date.
Alright, now you should have your color layer selection made, the next step is to lay down your opaque background. Generally I choose a medium gray so that I can lay out my values. After this, be sure to keep your color layer selected or create a layer mask! If you get annoyed at the little ants that march around your selection you can turn them off by going to View > Extras and unchecking Extras. If ever you accidentally deselect, simply use the Select > Load Selection tool on your color layer again.
After you've chosen your opaque color, it's time to start the actual painting. For this style, I tend to start with simple black and white and gray values. The majority of my art is painted using Photoshop's default hard round brush with the opacity and flow settings on. Simple! To begin, I simply paint softly starting with white and eyedrop the colors in between over and over until I smooth things out. I NEVER use the smudge tool for shading or blending. While it can result in nice work, it generally looks cheap, messy, and extremely unprofessional.
So, after a long time spent blending and working on the highlights, I might go in and add some darker areas if places need some greater contrast. Once this is done, I make sure I have my color layer selected and then I create a new layer on top with the blending style set to either Color or Overlay (generally, Overlay looks better). On this layer, I'll begin laying down my colors either by simply Filling, or, if variation is needed, by painting it in with a brush. A good hint here is to select your Eyedropper and set it to choose colors from only the Current Layer. This way, you can move colors around on your current layer without having to change the layer style to get the one you want.
You've probably noticed that once the values are laid down, the rest is going to go pretty quickly. After the colors are laid down, I tend to create a new layer directly under the line layer. On this layer I'll pick a bright color (usually white) and I will choose a very large, feathered brush. Using quick, soft dabs and strokes, I'll add soft highlights to areas that could use a bit more "pop."
Once that's done, there's only one thing left to do... the final details! I create yet another layer on top of all of the layers and I begin picking out and repainting the important details and making them more prominent. I also add things such as light reflected off of objects, wrinkles in skin, scars, highlights and colors on the eyes, etc.
So, that's about it for now. Please feel free to sling questions my way if you have them!