Basically, the base layer is just your normal preset files you colour for basic presets. So, your preset_1body picture that you paint over, that is your "base" layer. "Save as" these files before making your markings (as preset_1body, or whatever).
The markings are just on a new layer overtop of the base layer. Say, you want to have glowing stripes on your legs. You will first create a new layer over your body layer (this is using Photoshop). You make the markings on the legs on this new layer. When you're finished, delete the base layer (the body layer) and you're left with just the markings with a transparent background. Then "save as" as preset_1bodymarking (or whatever you want).
