You simply purchase them as part of the check-in process. Your room key will be encoded with the info, and you use it to enter the theme parks and water parks.
Although there's no guarantee, you should get 10% off the list price since you're staying on points. Also not guaranteed, but almost always available, is the ability to drop a day from the pass. So suppose you're staying for 5 nights, but you arrive too late to go to the parks. The CM checking you in will usually let you buy a 4 night pass, a considerable savings.
A really lucky guest will be given the opportunity to drop the first <u>and</u> last day, but you almost are given the chance to drop one <u>or</u> the other.