I agree, don't worry too much about it yet. 
However, yes you apply before you receive the ENTER, but you can change preferences afterwards. If all the course requirements are way above your actual ENTER, I'd assume that unless you were really lucky, you probably wouldn't get an offer. That's why it's important to have some lower scored backup courses that can lead to your desired course.
She's pretty much summed it all up. Basically, you'll be highly recommended by your Careers Advisor (or whatever they call it at your school) to put either uni courses with a very low ENTER requirement or TAFE courses as your backup since you can put down a maximum of 12 preferences.
From memory, I think it costs like $25 to apply and another $10 if you want an invoice. Also, my advice is to do it as soon as possible. At the time when VTAC applications are open, you're most likely in the midst of doing SACs and the least thing you want on your mind is forgetting to do your preferences by the due date and have to pay a late fee.
Also, if your school doesn't purchase the VTAC Guide for you, you will be highly recommended to buy the VTAC to assist you with your preferences. The VTAC Guide lists all the requirements to enter all uni and TAFE courses at every Victorian institution.
Once I again, I will reiterate: You are in year 11. This long post might seem overwhelming for you but believe me,
do not stress. Your school will do its best to assist and guide you in every possible way.