On the scanning part, if its black ink on white paper, just scan it as a bitmap, bitmap only makes 2 colors (black & white), if your scanning a pencil drawing that isn't dark enough just scan it as a grayscale, use levels to make the whites brighter and the darks darker, than save as a bitmap. I learned this because I'm always making rubber stamps with peoples signatures.

When you scan your drawings in, it is better to have a scan that is very contrasted, because otherwise your grays and erase marks will get in the way of your results (that is if it's only line work)

[Mac] Once you scan in your drawing, go to channels ...

hold the apple key while clicking any channel ... this selects all the white on the drawing

inverse the selection (apple+shift+i) ... now you have selected all the black

from this selection, create a new layer (apple+option+j) ... These are your lines separated from the

It will prompt you to name it, doesn't matter, whatever you like.

It may come out a little light .... if this is the case, fill it with black (apple+shit+delete)

Ink obviously works better ... you will likely have to do some levels adjusting if it is in pencil. Paper also makes a difference, but eventually you will get the results that you want :)

Anyway ... this is how I prefer to do it.

The way I understand your question, you are scanning in linework, and you want to create a color illustration from it. I do this in Photoshop all of the time, here's how. Make sure your linework is on it's own layer. Set that layer's blending mode to multiply. Create layers underneath that layer and begin adding color. The lines will still show, but you will see the color underneath. If you want the lines to disappear, move your color layers above the line layer.

If you want to fill areas with color you can do that too. Choose the Paint Bucket Tool, and make sure the "All Layers" option is checked. Go to your color layer and fill. This method will keep the color separate from the line layer. If too much area fills, go to the line layer and close any "leaks" in the linework. Use as many color layers as you need, but I have always found it best to never add color to the linework layer. The reason is that each layer has it's own mask. By using color layers with a strategy, you automatically create selections that can be used for fine tuning your illustration later on.

What I do is draw my Illustration and then take apic ( as i find a picture of my drawing is somewhat better than a scan) then I create the line work and colouring ( basicly everything) in Illustrator.

Doning it this way alows me to experiement as i go, finding new techneques and styles as i work towards a finished piece.

Do you know how to use the pen tool? If not that would be a great place to start. Using the pen tool, tract the key elements of the original drawing, this then allows you to turn your paths into separate layers with masks. With out seeing you original scans it is really hard to understand exactly what you want to do, but I have found that the pen tool, although hard to get use to, is one of the most useful and precise tools for making selections within PS. Live trace in illustrator may give you a basic start, there are a lot of tuts on the web.

The above suggestions are all great ones. Another way to give you control is scanning in your drawing. If it is black ink on white paper, play with the levels to get as close as you can to pure white and pure black without over-pixelizing. Then go to Select > Color Range... and use the eyedropper tool to select your background color. This will select all the instances of that color range in your image. Then you can delete your background and your have your linework on its own layer. To get a more solid black (or whatever other color you want) you can put a color overlay effect on the layer.