Nice to hear about your project! You could look at the tutorial by Simon Greenhill and Konstantin Hoffmann
here to get you started with tip-dated nodes. It might also be helpful to look at the .xml files from one of the recent phylogenetic analyses of these languages families (if they were done in Beast). You can find a whole list of papers on Austronesian and Pama-Nyungan phylogenetics
here. I am not sure how helpful I can be but happy to talk by email if you have any particular problems.
Best,
Rehan