when you filled in the tax file number declaration form you should have filled it in as not being on your tax free threshold, cos technically you're only supposed to have one job on that at any given point of time.
The second job will then get taxed at a much higher rate, while the first stays on the normal rate. At the end of the financial year, you will get all the tax you paid back if you earn under the tax free threshold, which is $6000, and any more above that will get taxed at the normal rate.
Hmmm i basically repeated what others have said... oh well. I know that's definitely how it works!