Getting Started
The medium I use on the computer is Adobe Photoshop Limited Edition (LE), a somewhat old program. It's not exactly like the full version of Photoshop (especially the newest versions), but they share many features in common, so I will be speaking about it as if it's Photoshop itself. However, no matter if you work with Painter or Photoshop or Paint Shop Pro, the basic principles of shading are all the same. If you learn to understand the concepts behind the painting process, you'll be able to create great works with any medium.
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Layers are a computer artist's best friend. Photoshop has many modes of combining layers. Some of the more important ones are:
Normal - whatever's on this layer will cover over the ones below
Multiply - the colors on this layer will "add" to the ones below; black darkens to 100%, white does nothing
Screen - the colors on this layer will "subtract" from the ones below; white lightens to 0%, black does nothing
Overlay - the colors on this layer will be mixed with the ones below to reflect the darkness of the colors below
Soft Light - gives an effect somewhat like shining a colored light onto the layers below, just like its title says. Good for special effects
Color Dodge, Color Burn - not unlike the Dodge and Burn tools, which means they are usually baaaad. I will go more into this later.
Difference - creates "negatives" of the colors
Exclusion - Works like Difference, except "not as severe". I don't know what that means, but it can be useful for effects, and is not as harsh as Difference.
Your graphics program might not use these terms, but you can probably find similar features. Check out the Help file, it will mostly likely have sample images of the blending modes in action.
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There's no hard and fast rules to how you should use these layers, and sometimes I'll switch between various layering modes until I find one that gives the best effect. But here's a very basic, rough guide to what's best-suited for which purposes:
The picture's outline can be on a Normal or Multiply layer, depending on how you want to go about things. More on this in the next section.
Base color (the main color of an object) can also be on Normal or Multiply, depending on how you have your outline set up.
Shading definitely goes on Multiply. Not much question there.
Conversely, highlights would be on a Screen layer. However, it's also possible to use Overlay, Soft Light, or even Hard Light, whatever looks best to you.
If you don't see how this works, just keep reading. I'll go into more detail in each respective section.