The way I go about creating a spec map is like this:
Use the default spec map to create the new file. Load it into your graphics program and save to its format. The default spec map has the items like gear and cockpit parts that most people don't skin so this will form your base layer. Next open your skin's bmp file in your graphics program and copy and paste it as a new layer. This layer is just used to line the other layers up correctly and is turned off once the spec map is done.
Then you can import layers directly from your base skin. The base paint layer, the panel lines, paint chips, chipped rivets and so on. Bare metal skins have a light base layer and then a dark paint markings layer on top. I usually add the gun, exhaust and oil stains as a dark layer, you can see this well in the new Stuka screenshots, on the wingroot. Dont try to cram everything onto a few layers, it is much easier to edit if every effect is on its own layer. On a spec map i usually end up with about 20 or 30 layers. Most of these are just copy and pasted from the base skin though.