Hello, Denise!
Not to worry!
While Walt Disney World constantly monitors
Resort Transportation usage and adjusts schedules accordingly, such transportation will always be available an hour before the parks open and at least one hour after they are closed. This means that Resort Transportation will follow that schedule based on Extra Magic Hours as well, since those parks are still open during those hours. As always, if a monorail is not running for any particular reason, Resort buses and ferries remain in place in order to help Guests get to their desired location after park close.
Extra Magic Hours are often adjusted based on factors such as holiday weekends, special park events and other elements which might bring more Guests into the Resorts and parks alike. As such, it's always a good idea to check each park's calendar, available through a link on their webpages, to see if park hours and / or Extra Magic Hours have been adjusted as the day of your arrival gets closer.
Hope that helps! Send more questions as you think of them. We love to help!