Alnina,
If you get an offer for enroute, you'll be told where the training is and where your final posting will be. If you get a Brisbane course, you'll most likely be posted to Brisbane. If you get a Melbourne course you could go to either, but you may have a choice. That said, it was two years ago since I went through the selection process, it may have changed.
I initially applied for enroute, but when I was offered a place I requested tower and ended up on a tower course. At the time, we were asked our preferences, but the chances of going where we wanted were pretty small. Had I made it through the academy, I would have most likely ended up in Sydney, or Bankstown, but one of the guys on my course did end up in Perth.