Hello Callum Here!
I understand i may not be the most experienced here on PMC but i still now how to make skin's.

This tutorial will be showing you some different shading technique's:
Realism
Boxing
Below i have a basic image of a normal skin without any shading at all
http://www.planetminecraft.com/skin/shading-with-callum---example-skin-no-shading/
We are going to make this skin 10x better with only shading!

Boxing!
Boxing is probably one of the easiest ways to shade a skin
in MCSkin3d select or make your skin
Next got to the Dodge/Burn tool
Select burn
Then carefully go around the edges of each part/box
And you should end up with something like this!
http://www.planetminecraft.com/skin/shading-with-callum---example-skin-boxing/
Realism!
Realism is one of the more harder shading technique's but its not really that hard just a little bit harder than boxing
in MCSkin3d select or make your skin

Next got to the Dodge/Burn tool
Select burn
This is where its up to you and what you think looks best
Shade in the areas you want
NOTE: Try and make it look realistic eg. if the hair is flipped right make the direction of the shading towards the right
And you should end up with something like this!
http://www.planetminecraft.com/skin/shading-with-callum---example-skin-realism/
It is actually as easy as that!

OBVIOUSLY YOUR'S WILL TURN OUT BETTER WITH A LITTLE BIT MORE EFFORT THAN MINE :P