Theme folders should be in /Library/Themes and end with a .theme suffix. (Worth mentioning: make a backup of this before messing around with it.) I don't really know much about Winterboard--although I've changed my SMS sounds before via SSH, this was my first time altering a theme, and I was surprised at how easy it was.
Basically, once in the folder I copied the LockBackground.html file, opened it in WordPad, and made the changes I needed to make so that the theme looked in my native files for which wallpaper to use. (My issue was for the lockscreen, not the home screen.) With that done I copied the edited file back into the folder, replacing the original. After respringing, I was done. If you have trouble, be sure you're replicating everything you need to as far as formatting goes (quote marks, parentheses, etc). The file you're looking to use as a replacement is probably something like this: "/private/var/mobile/Library/SpringBoard/HomeBackground.jpg" Good luck!