Hi Peggy - There is definitely a lot of conflicting information about how to optimize Extra Magic Hours, but a lot of it depends on your particular situation. Personally, I like to visit during Extra Magic Hours only, and then visit a different park during regular park hours. But, if you don't have the park hopper option, you won't be able to do that.
If you don't have the park hopper option, then I'd recommend visiting the Magic Hour park only if you plan on taking full advantage of the Magic Hours.
As for the Walt Disney World Railroad, it runs constantly and not on a specific schedule. There are three stops, including one right at the front entrance of Walt Disney World. The other stops are at Frontierland and in Toontown.
If you'd like to learn more about the Railroad,
visit this page on the Disney website.