I have never seen anything for a res folder in the "themes" folder at all. I just put all my icons in the local/dmenu/res/emulators folder.
Are you using Toddler's local pack, or the booboo one?
I'm pretty sure I use Toddler's pack...and, as far as I can tell, I only ned to put my icons in one place. Then again, I haven't played around much with Themes, I could honestly care less about Themes...I'm more interested in looking at games than fancy wallpaper...so I only use the default theme.