Ahh, yes. There's something very honest about the manga style of drawing, and this is one area where Photoshop rocks.
Start by experimenting with the layers pallete. You'll find you are able to make a copy of your image by dragging its layer to the new layer button. You can then work on your copy, and if you muck up return to the previous layer.
A good method I've found is this:
- Make a copy of the original image as a new layer. Turn the original layer invisible.
- Go to Select -> Color Range and select the highlights, so that you're left with only the dark pen lines not selected. Then, press delete. The background "checkers" pattern should show through, so that you can see that all the white of the paper is gone, and only the pen lines remain.
- Make a new layer, call it Color (or Colour if you speak the Queen's English). Put it behind the layer with the pen drawing, and then use the brush tool to add colour.
By doing this, the brush will not erase your pen artwork, allowing you to fill the empty regions with colour and patterns to your hearts content.
Another method, with a similar result, is to paint the colour on a new layer with a blend mode for that layer set to "Darken", "Overlay" or "Colour" (You'll need to experiment a bit to get a feel for what works on what type of scan).
Another easy method is to create a new layer for your colour, then create a copy of the artwork and put that on TOP.
Set the artwork layer on top to "Darken"
Then, select the colour layer and fill it with white, then start painting the colour in ON THAT LAYER.
Check the tutorials thread for a list of dozens of sites hosting tutorials about PhotoShop.
Oh, and if you happen to have cash to burn, get yourself a Wacom tablet... these make it easy for you to redraw and adjust your artwork in PhotoShop. They are expensive, though, so maybe you could put it off till you sell your first book.