The correct way to lodge allowances is to add your total allowances to your gross salary.
Then you claim the max reasonable amount back for every night you were away.
The ATO views allowances as income. They also want to see what you spent it on. If you don’t keep a travel diary and you do get audited, they will treat your allowances as income and they will tax your marginal rate on it.
Hence why you need to declare it.