You'll need a gfx app that handles layers (and PSD files).
Each section on Bunta's skin kits are on a separate layer meaning that you could strip the lot down to a plain white skin if you hid / removed the other layers, but the others are there to guide you.. the wireframe in particular is _very_ useful to helping to align logos / design elements of your skin.
In short, you paint on a new layer _below_ the mask, wireframe and shadow layers, then once you're done, hide the wireframe and save as a DDS file. You'll end up with a skin usable in LFS with the design you expect.
This is the basic concept of the skin kits anyway.. and once you understand how they work, you'll find them a _lot_ easier than a default plain skin to work with
Regards,
Ian