Believe it or not, the ATO are generally helpful with these sorts of questions.
Not sure if they are still doing it, but when I had a sole trader business, they sent out an adviser to help. Though this was when the GST was new.
But basically you register for GST, charge it on your sales and claim it on your purchases. This is done through the Business Activity Statement, lodged quarterly usually.
If all your income is from one company, you cannot claim expenses for anything other that what an employee can claim. (This is to prevent employees from becoming sub-contractors and claiming for every thing including cleaning their toilet at home ;)
The equivalent of income tax for s aole trader is PAYG (pay As You Go) - you pay tax as you go depending on your income. The ATO might even ask you to pay tax up front, depending on your income.
I did it for about 8 years - a bit of paperwork around BAS time, and end of year.
