Yes, so some unis will make you use two preferences if you want to apply for both bonded and unbounded and some don’t, but will perhaps ask for your preference in the direct application, or just offer you what you’re eligible for.
As for how you preference things, I think you just put them in the order you would prefer them. There are rumours that go around every year that JCU only interview people who have it as their first preference and every year people who have it as their 4th or 5th preference get interviews, so don’t be swayed by those if you see them floating around!
Re: length of degree.
UQ 3+4 (minimum)
USC 3+4 (minimum)
Griffith 2+4 (minimum)
JCU 6 (minimum)