writing a script is difficult enough itself. can't imagine how difficult could it be following a non-linear order..
probably the best thing to do is to write down a scheme with the basic structure of the movie, first time following how the events will appear with the finished product, then in chronological order, just to fill in all the links and be sure that nothing's out of its place.
Then the script can begin with the real order (the non-linear one).
Me and a friend of mine tried to do it: I'm still writing down mine, and i have to admit it's very difficult, because I'm focusing on what can keep the audience concentration high without annoying them (and maybe surprise them with cool cliffanghers).. hope i can finish it soon.
My friend finished writing and even shooting.. he changed many details during shoots, and his short became more complicated than it was before.. if i didn't know the story, i wouldn't have understood when i first watched it.
that's another important thing.. movies like Memento or Following are brilliant because even if they're difficult, you can find out an interpretation (one of the several..), and after 2 or 3 visions you can understand pretty well. Some movies (i think about Lynch..) are just impossible, 'cause probably even the director didn't know exactly what to tell (see Inland Empire..) !!