i too have had trouble but it all seems to work for me now - the plugins are now a part of moonshell and will stay that way - whatever is in the plugin folder thats found inside the shell folder seems to be incorporated into moonshell. For me, being an sc card user, when i run the setup i export it to my sc card, so it copies over the boot.nds as well as the shell folder.
for us it is very important to include the shell folder in the root directory.
if you wanted to skin your moonshell, copy over the new image files into the shell folder to replace the old, then run the setup again and put hte new boot.nds ans shell fodler on your card.
i'm not sure if this will help or if this is specifically what you are asking - hope it helps a little though.
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