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First, I'll sketch out the art on paper using red pencil.
Then, with a second piece of paper and a light table, I'll ink over the redline with a black felt pen, usually a Pigma Micron. Here I used a size 08.
Next, I'll scan that in at 300 dpi using the "black and white drawing" setting. This gives me a huge image, but it is pure black or white (no shades of gray * ). Of course, this is well larger than my final will be and has a stair-stepped line, but it allows me to color it without that white anti-aliased halo around the linework. Once I color it, I'll shrink it down to final size.

Once I have the scan, I open it up in Photoshop.

First, I copy and paste the original onto a new layer, so I can preserve the original incase I mess up the copy.

Second, I use the wand tool to select all the white. Be sure the wand has anti-aliasing turned off, tolerance set to 0, and contiguous is turned on. With the white selected, delete it, so you end up with only the black lines.
Once you have this layer, lock the transparency by checking the box next to the checkerboard icon at the top of the layer window. This will prevent you from accidentally filling in the transparent areas.

Now make a new layer and call it "color" and drag it below the line art layer. Do all your coloring on this layer. Since
the line art is pure opaque black, you can select transparent areas using the wand tool, click on the color layer, and fill in the area till you end up with something like this.
I usually create another layer below the color layer for a background.
Here is a screen shot of how I've set up the layers so far.
At this point, I'll usually save and "save as", so I can combine layers without destroying the seperated file.

The final art looks like this.
I added an orange outline by combining the blackline and color layer and then opened up the "layer style" box by double clicking on the layer.

In the Layer Style box, check "Stroke" and then click on the stroke bar for options.

Once you combine the ink and color layers, you can shrink the image to any size you want. Make sure to combine the layers first, cause sometimes Photoshop will have problems with lining up the seperate layers perfectly and you'll get a little ghosting around your linework.
Lesson 1: Basic inking and painting.
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*This actual image has been
scaled down (and thereby anti-aliased)
for the purpose of this tutorial.
The original is 846x1090.