Rough drafts are done quickly and in large numbers. I don't make a huge deal over scanning, more often than not I just take a photo with my smartphone then use that as a starting point.
I pencil out the shadows and dark spot in red pencil. 80% of my inking is done in Manga Studio 5
I put down the initial line work and make any subtle changes on the fly
I delete the pencils and finalize the lines doing touch ups by jumping in and out of Manga Studio and Photoshop CS6
Watercolors are laid down with some of my own personal scans from life and some other brush work in Photoshop. I stick with photoshop for my coloring most of the time!