Using the magic wand tool (you can't miss it- it's a magic wand) with a tolerance at around 80-120 on the tool options palette, click the “merged” layer and click the first place you want to color in your image. It is now selected, and only areas within your selection will be affected by the tools you use. Holding shift while making selections allows you to select more than one part at a time. Flood fill in your selection with the base color you're using. The base color is the lighter of the two colors. The shadow color is the darker.