Most peopel I hear that start in Perth go North... I would actually suggest this as hen you are going with the vast majority of people in the same direction... you bump into friends in towns along the way and it does actually help you and them! :-)
I would recommend getting a campevan yes, especially travelling anywhere but the east coast as you can stop anywhere to sleep and sights a far between. I foudn this page for you that should help:
http://www.australianbackpackers.net...-rent-sale.php
Also as you are going to the Northern Territory I felt I shodul recommend to you a really great tour guide operation that runs all different types of tours not just canoeing... check out thier NT guide here:
http://www.geckocanoeing.com.au/info-darwin-city.php
Happy travels!
brad