To prevent making a huge mess when writing fingerings, only write in shifts or extensions. If you need to write fingers for every note, chances are you need to study the geography of the fingerboard. To do that, just make sure you know what note you're playing when you put down a finger (best thing to do is say the note out loud after you play it). Also, try to stay in the same or close positions for as long as possible (your arm can get tired and it makes a mess on paper).

I'm not sure how advanced you are, so I just gave you what I'd tell a beginner.