As of yesterday (7/18/10) Disney made an excellent change to how they accept reservations.
In the past, if you wanted to book your room in advance, you had to book it as a "room only" reservation. There were two problems with this: 1) You had to pay a full night's stay deposit 2) When you were ready to book a package, the travel company had to cancel your room only reservation and rebook it as a package.
Thankfully that has changed! You can now book your rooms early with a "basic" package. Essentially, the Basic Package allows you to book your room as a package so when future dining/ticket prices come out, you can simply add those on to your package. There's no longer a need to rebook - you keep the same reservation number. And the best part? You only have to pay the $200.00 deposit.