Your Park Hopper means you can go to as many of the four main parks in one day as you like and it still is one day--including EMH.
The options (used to be called "Pluses") are individual--once used, it's gone. If you go to two of the option venues in one day, you use two options.
The options are for the water parks, DisneyQuest and PI (until it closes). Can't remember if miniature golf is included--we just get park hopper tickets.