Start by scanning your linework in black and white. It's up to you how to handle it: You could either sketch and ink a hardcopy for scanning, or scan your rough and trace over it in photoshop. Whatever you find easier. There is some contention on what you could do next. Some people prefer a very clean line, so if you have Adobe Streamline you
could import the scan into Streamline and essentially vectorize it, which will smooth a great deal of the imperfections created by the hand. I actually like the look of rough lines, so I leave those in. Whatever you do, make sure the linework is black and white and set it to the top layer in Photoshop. Change the layer's blending mode to "multiply" which makes all the white areas transparent. For the coloring bit, make separate layers for each base color. In other words: "Skin, Hair, Pants, etc." Make sure you clearly label each layer, it will save you a lot of agravation later. Color each area the base color, making sure to stick to each color's designated layer. You can use paths to define an area and fill it, but I would suggest doing it manually with the paintbrush or airbrush tool. The practice will make you better with a mouse or stylus. From there you add details as necessary .
For a more detailed description, check the tutorials on this page:
www.sijun.com. I don't like this guy's drawing style per se, but his talent for coloring is awe-inspiring. And his grasp of composition and lighting is very impressive.