Sometimes you can get better results by leaving "Use smart recolouring" checked, unchecking the 2 sliders on the right that default to "Automatic", and moving those sliders around. It kind of depends on how much variation is in the skin's colors. Looks like the color you're wanting to change is green, so I'd scoot the "Primary skin colour" slider over to the green section.
I don't know if you can define a primary skin color in SkinStudio. It seems like I may have seen it at some point but I couldn't begin to tell you where or even for sure that it's there. Some one else might know.
