Looks like you're off on a good start for a first repaint.
Oh and don't worry about the questions, always happy to help.
In the lower example, where you are seeing the shading on the Doctor-Heli repaint, that is shading applied to a layer above the other repaint layers. This is much like the process that is used by profile artists to create depth. This is done by applying highlights on the upper sides of surfaces, and some darker shading on the lower sides of curved surfaces. You can give this a try and see how the effects work, just use a new layer on top of the stack that you can experiment with.
I'll work up a sample to illustrate what would be a beginning way to try this.
