Just replace them all manually. I stopped using winterboard a LONG time ago, it just slowed down my iphone too much. Plus I like choosing which icons specifically are replaced and I like making my own custom icons. It's also cool to replace your unlock slider and stuff like that.
Problem with that is u lose the icon when the app is updated- as far as customizing, using an icon folder in a theme is the best way to go as far as building a repository for your custom icons