My whole process usually takes place inside photoshop. Sometimes I might draw a sketch pass on paper and scan it but since I'm on summer break from school I don't have a scanner. For my comic, I've been using a method I like to call "Storyboard" shading. I use very stark values with minimal gradation. I draw the final ink lines, make a new layer under it, block in the shape with a base value, clean up the blocked out shape to fit the lines, lock the transparency, and then paint in my shading. For color, I make a color layer above the grayscale shading layer and set it to Multiply.
It's a somewhat quick method for me... but that might be because I previously spent an entire month solid doing storyboards until I was absolutely sick of drawing for like 3 months after that.
I might actually try a new method for the next part of my comic because I'm starting to feel this doesn't look as "clean" as other peoples' comic coloring techniques look.
I'm really interested in learning more about your method.