The experimental editor in the garage is understandably buggy. One suggestion would be that implement a skin editor. So you get a window with the car skin just like if you use paint.net. And when you save, you name it, and all get sorted out in the jbeam-files. No coding necessary. Or if that is too much, an export/import option or plugin that gives you a PNG file (and aditionally colour map, uv map) of the skin. Then when you have edited it in a separate program, you just press import- get option to name it or over write an existing, and all code be generated in the background. Or maybe someone already have done a tool like that?
At this point, just use a skin template (there are plenty online), or make your own. Maybe a few more clicks, but you suggested using paint.net anyway.