Well, the question is how precise do you want to get? If you want precise pitches, then you have to write down pitches of course, like in the way Christopher Dunn-Rankin mentioned. If you want to use it more as a "sound effect" where the actual pitches don't matter so much, you could go for a more graphical notation, with a wavy line designating how high the overtones should be, which might faciliate the learning process for the didgeridooist (is that a word?). But it will make your notating process harder if you write it in a common notation program

Or you could just write down the "vowels" which should be formed, maybe even with the phonetic alphabet or something. (But I don't know enough about the Didgeridoo to be able to say how well this works).
But in the end the best thing is to get in contact with someone who plays the didgeridoo, show her or him several versions of your notation and ask how s/he would read them and whether it's understandable. Even if you can play the didgeridoo yourself it would be good to ask someone else and see whether they can make any sense of your notation.
"Exotic" instruments like this simply don't have a standartised form of notation, so it's crucial to work together with performers. Or at least be as clear as possible with whatever notation you decide on and explain it in the preface.