Are you talking fixed moorings or dropping anchor?
It really depends on which direction the wind is blowing there are heaps of different options.
Also the Rottnest Island Authority has moorings (the green ones) in most bays that you can hire on a daily basis.
Beware that for some reason anchors seem to drag easily in Parakeet Bay, I skippered the sea rescue boat over there for a few years and dragged a number of boat off the beach both there and between the Army and Natural jetties in Thompson Bay.
The thing to watch out for is the wind swinging overnight i.e. in summer it is usually blowing SW at sunset but swings to strong SE/E/NE sometime overnight that is when the anchor can drag.
Some people set two anchors to cater for this but this can cause problems if you are anchored near others that only have the one anchor set.