When you book a room only, you get exactly that, a room. You have to pay one night's deposit and the rest at checkin. Now if you're booking the room only to convert to a package when they come out, Disney has to cancel the room only ressie and rebook you a package. If you're going at a very busy time and are staying somewhere very popular you may not be able to get the same room back when you book that package.
The basic package is a room, no tickets and some other little amenities like WWS admission and/or mini-golf. If you have one of these, when the "regular" packages come out you can call and just modify this ressie and keep the room you are holding. You will be required to put $200 down and pay the balance 45 days prior to checkin.
Hope this explains it.