As for how voting works:
For the House of Representatives [2], each person is voted in preferential order. Each candidate must be allocated a preference or else your vote is informal and not counted.
For the Senate [3], you may either vote 'above the line' or 'below the line'. Voting above the line involves voting for a party. That party then takes your vote and distributes it amongst the preferences they decide. You cannot indicate preferences above the line - you must vote for a single party and the party then does that for you.
Voting 'below the line' involves marking each candidate from each party. They are still grouped in parties but you may number them in any order, so long as you number them all.
I am not sure what being a party vs. being independent. Independents can be elected to both houses, so I do not quite know what being in a part achieves. The AEC website doesn't obviously offer any information detailing it, at a casual glance.
[1]: http://blogs.usyd.edu.au/cru/2013/04/senator_assange.html
[2]: http://www.aec.gov.au/Voting/How_to_vote/Voting_HOR.htm
[3]: http://www.aec.gov.au/Voting/How_to_vote/Voting_Senate.htm
For this reason the incumbent independent senator Nick Xenophon has registered his own 'party'[1] -- the Nick Xenophon Group -- and will now appear above the line as well.
[1]: http://www.abc.net.au/news/2013-07-02/nick-xenophon-has-poli...
The upper house (or senate) seats are allocated to parties based on proportion of total votes by state. My understanding is that wikileaks is hoping for a seat in the upper house as do most minor parties is Australia. So the government needs to negotiate with the minor parties for legislation to pass the upper house.
Unless I think, in the case when the elected party have the majority, which is a possibility after the next election.