The first difference to realize between making colors in Blender for 3D printing and the usual way of making colors in Blender is that you have less control. All you can control is the diffuse color. You cannot make the object shinier by adjusting the specularity, you cannot add transparency, or any of the other controls. In this respect, a 3D printer is like a regular printer. All it understands is a colored pixel. If you use transparency, at best it will show you the bare physical material underneath. Shininess, specularity, and so on are all properties of the material that you are printing with.
There are three ways to color your model: