Hi, Melissa. Long time Pop Century fan, first time answerer of your questions.
The only Disney Transportation system option for Pop Century is the bus system. The busses will take you to the four theme parks, water parks and Downtown Disney. The easiest way to get to Magic Kingdom is to take the bus directly to the park. It lets you disembark just off to the side of the theme park's entrance.
The monorail and ferry boat are transportation options for those driving to the park and parking at the Transportation and Ticket Center (TTC.) Unless you'll have a car, it really would be an unnecessary stop for you.
There are plenty of other opportunities to ride on a boat, including the
Liberty Square Riverboat within Magic Kingdom. You can easily ride the monorail too by picking it up right outside the gates of Magic Kingdom and Epcot. We like monorailing over to one of the monorail resorts around Magic Kingdom and having a meal there (Chef Mickey's, 1900 Park Fare, etc.)