I usually label this first scan as my "B&W Master" drawing. I check it for flaws and do a few onscreen touch-ups if necessary. Then I create the differently named copy (FILE>SAVE AS...) that I will use for the actual coloring.

I reduce the copy's resolution (IMAGE>IMAGE SIZE...) to 300dpi (the resolution commonly used by magazines) and change its mode (IMAGE>MODE...) to either CMYK or RGB, depending on whether the drawing will ultimately appear in print or be displayed in pixels on a computer screen. (You can't convert directly from a bitmap image to CMYG or RGB, by the way. You have to first convert to Grayscale and then complete the change to color.)