Rather than go back and forth about whether you should book with a travel agent, I thought I'd give you some practical information based on my experiences travelling to Oz.
I was originally considering a package offered by a travel agent which included airfare and hotels in three cities. When I was told, "no hotels are available for the dates you want to go" I said "The heck with this I'll plan it myself." I ended up spending much less money, tailoring the dates and durations of stay in each city to my specific interests, having a blast, and having the thrill of experiencing and discovering things on my own. Do the reasearch first to find out what locations and activities appeal to you. Then, you can make a more informed decision if you decide to go to a travel agent, and you can book on your own if you prefer.
Check out several websites to get an idea of the airfare you should pay for the dates you want. Try
www.orbitz.com, www.travelocity.com, www.itn.com even
www.hotwire.com if you are flexible about times. Also, go straight to the major carriers (Quantas, United, American, Air New Zealand). Sometimes they run specials on specific routes.
I assume you want to dive. If you really want to see the best of the Great Barrier Reef you will want to do a liveaboard. Take a look at these websites to find out about boats:
http://www.explorerventures.com/ (Note, they have a green season special. Rain is more likely in the green season. I went to Oz in the grean season and had no problems with rain. On a diveboat, it doesn't really matter if you get wet anyway.)
http://www.mikeball.com/ (Note: The dive master with the diving operation I used (a competitor) told me that this is the best dive operation on the Great Barrier Reef. Book with an Australian travel agent if possible because the price is higher for Americans.)
http://www.cairnsinfo.com will give you an idea of the lodging and activities available in Cairns, the jumping off point for the reef. I can personally recommend the Tully River white water rafting trip and Jump the Beach skydiving in Misssion Beach.
Also take a look at
http://www.travelmate.com.au.
There are a few other websites that I used when researching my trip but they are on my other computer. I'll see if I can find them.
By the way, if you're at all interested in Tennis, go in to Melbourne in Januray and take in a few sessions of the Australian Open. Ticket prices are quite cheap and it's possibly the best outdoor party I've ever attended.
I'm so jealous! I wish I was going with you!!!!