Some time ago I wrote up some instructions for using DuckDuckGo as the main Safari search engine through a little SIMBL plugin called Safari Omnibar. Personally, I’m not a big fan of using SIMBL, it’s just that at the time Safari Omnibar provided something I couldn’t be without otherwise. It’s come to my attention (via Stephen Hackett) that there’s a standard Safari extension called Omnibar that accomplishes something similar.
Follow Marco Frissen’s instructions to get it. After installing the extension you can simply choose to add DuckDuckGo as your default search provider in the extensions preference tab in Safari.