After reading the Basic Gimp Tutorial you can proceed with playing with layers.
You can get freely the file herewith used as example from the Shop (free registration required).
Download the SkeleToon Demo (800kb)
Once opened the file and the Layer Window ( [CTRL] + L ) you will see this:
On the Layer Window you will see several eyes
; clicking on those eyes you can see or not the relative layer. In this way you can change what you see on the main window. With our example you can have the SkelToon with a shield or a sword in both hands; or you can have or not the helmet. Each time you act on a weapon layer, you have also act on the flame border as indicated by the arrows. You can even switch off entirely the flame border and put your own style.
Please, remember to click on both
Front and Back layers.
When finished, merge the whole by a right click on a layer and choose the Flatten Image
You can now Save the image in your preferred format.