I've done it both ways dependent on the vacation and what I'm willing/able to spend. First, you should never pay a
travel agent for their services. They receive compensation from their clients (Disney, hotel chains, etc.) for their services.
We are also going in June 2013 and are planning to stay at the Polynesian. Because this is a popular and pricey resort with limited discount opportunities I decided to go with a TA to help me. I am going to use
Dreams Unlimited since I love the Dis, Dis podcast, WDWinfo website and I trust their information and expertise. So, when a discount comes out that I qualify for, my agent will be my advocate and apply whatever she can to save me money on my trip. I'm not removing myself from the equation but having an expert out there to lend me a hand isn't going to hurt.
The last two years we stayed at a moderate and value and I booked those trips on my own. The discounts were more broad reaching and I felt that I could manage that.
Ultimately it's up to you. Good luck and happy planning.