Taking for granted that you have scanned the job as it needs...
1. Change the colour mode of the picture to RGB.
2. The lineart is in 'background layer'. Change the name of the layer to whatever suits you (let's say 'George).
3. Make a new layer (call it 'colours' if you like) and put it under 'George'.
4. Put 'George' in 'multiply blend mode' (in the Layers Palette).
5. Start painting in 'Colours'.
That's the basic way. Adding more layers and effects and blah, blah... you'll get a better control. You might even like to use another program (InDesign or Illustrator) to combine the lineart in 1200 800 dpi and the colours in a much lower one (250 dpi or so)... or you might like to vectorize the lineart with streamline...
It's a whole world, but I hope this helps.
(Posted from Spain)