If you're modifying a skin from your skins folder or something, it is very difficult to maintain panel lines and rivets and what not. You cannot seperate those layers once the skin is in it's final state. Pretty much all you can do is paste stuff on top of the image.
You'll need a good graphics program that can use .PSD and .PSP files, the vast majority of templates are in .PSD format. It's template files that have all the various layers with panel lines, rivets, etc, etc as seperate objects. Once you have templates and the program to use them, then you can do what you want. It's real easy to add stuff and drag it down to the proper place in the layers. I use an old program called Corel Photo-Paint 8. I
think there is a program some people use called GIMP, might be free, not sure though.
You'll also want to grab something like BRIGHTER, which is available at
http://www.simmerspaintshop.com/. For the game to read a skin, it has to be an 8-bit paletted image. Where as when you're working with a template it's in 24-bit RGB color. BRIGHTER usually does a better job at converting than some graphics programs can do themselves.
DW