Hello there, wiggsama,
You're right, you can only track a maximum of 5000 kilometers per vehicle. If you maxed out the three vehicles, I recommend checking with a tax advisor. They will be able to give advice on how to go about reporting this information for year-end taxes.
Please see this article for more details: Automatic Mileage Tracking in the Mobile App.
See Australian Taxation for Business for more information.
I'll be right here if you have other questions.