Becoming familiar with the skin editor is not an easy task.
Let me first explain, how to create an empty skin. This must happen before you can map anything. I found a good description for that in an older thread:

"Here's what is working for me:
a. Open MED
b. Add model
c. Open 'manage skins'
d. Click 'new skin' (This also opens 'skin settings')
-- Click 'texture', click 'texture format'
e. Go back to 'manage skins'
-- Click the skin name in the list-box
f. Go back to 'skin settings'
-- Fill in the texture format boxes, then click 'OK' // 1024 * 1024 for example
g. Open the skin editor
-- You should see an empty skin, that's ready for mapping
h. Map away, have fun
i. Paint on the lines

Look at the bottom left corner of the skin editor. See four color boxes. Each time the skin editor is started, - left to right - these boxes default to red, green, blue, and white.

Box number two is the triangle fill color, when using the flood fill tools. Note that the box-two color will always fill the triangles, even when not selected.

Boxes one, three, and four are the line fill colors, when using the flood fill tools."

But now to your question:

Mapping a model:
1. Minimize the skin editor window.
2. From the model (or the group), select those faces, that are best seen from a certain angle (left / right / front / back / ...), and that should be connected on your uv-map.
3. Create MD2 mapping for those faces.
4. Maximize the skin editor. You should see now the faces that usually cover the whole skin. Resize and position them on the UV-map (does not have to be exactly, just to make room for the next mapping)
5. Hide these faces in MED. This will also hide the faces on the UV-map. If you skip this step, the faces will disappear, when you create the next mapping.
But now they are only hidden on the map. You can see them again, if you select "show all" in MED.And Hiding the faces, that are already mapped is also
good, because you see (not) what is already mapped.
6. Now you can proceed with the next part of the mesh. Select "Hide selected" after each mapping.
7. If your model is completely invisible, everything should be mapped.
Now you can select "show all" and everything should be there on the uv-map and can be arranged.
8. Before you export this to your paintprogramm, make sure, to paint the lines (see above).

I hope, I didn´t forget anything, I didn´t do it very often myself.