Unless you choose to utilize the valet parking service, there is no charge to park at any of the WDW resorts. If you are going to one of the monorail resorts or the BC/YC, you may be given a three hour parking permit. Disney strongly discourages people from parking at one of these resorts and then going to the parks. Too many people have been doing this and at times there hasn't been enough parking for the guests actually staying at these resorts. However, you are welcome to park at these resorts to eat or shop. Three hours should be plenty of time for that.
As the other posters have said, you only need to pay the $6 parking fee (for the theme parks) once per day. You can leave a park and return later or even change parks. Just save your receipt and show it to the parking attendant when you return or at the next park.