This is my understanding:
Is there a hidden "submit" button somehwere?
or are we automatically a timely applicant if we paid on time?
No. If you've paid, you've submitted. You should have an invoice confirming that.
http://www.vtac.edu.au/applying/courses.html#fee - It states that there about checking if you've paid.
Is that the $26 we had to pay? Our preferances aren't due tomorrow?
You need to have paid the $26, meaning that you've submitted an application, by tomorrow yes. Unless you want to pay the late fee.
You'll see this phrase crop up a lot on the VTAC site. This particular quote is taken from the footnotes on the important dates page.
"3 Final date to pay your course application processing fee. Only paid applications will be forwarded to institutions to be considered for offers. VTAC recommends that you pay early."
Are we allowed to add and/or remove preferences after exams, or can we only change the order of preference? If so, then is a timely application just about paying the money on time?
I believe so, timely application is mostly just about paying the money on time and getting some initial preferences in. You'll be able to add + remove preferences after exams (for most of the month of november you won't be able to though).
http://www.vtac.edu.au/dates/ Take a look at the dates 'change of preference' will close on 26 October (5pm), and then reopen 26 November (9am)
As far as I'm aware, there's some courses that you can't add after some particular date, because they consider early offers, or have interviews or whatever other random reasons.
I just googled for an example, and it appears Monash MBBS is one of those courses with a deadline date to be added onto your preferences: "Only applicants who have listed at least one of the Monash MBBS course codes (28251, 28151, 28691) by the late closing date of 9 November 2012 may reorder their preferences and/or add additional codes for Monash MBBS up to 24 December, 2012 (IB, WA, NZ NCEA applicants have until 4 January 2013)."
http://www.monash.edu.au/assets/pdf/study/monash-careers-update-2012-08.pdfedit: I've added some VTAC quotations