I did the 5K two years ago and plan to do it again this year. We started outside the park in the parking lot (near the starting point for the longer races), did about 1/2 the race outside the park through the backstage areas (behind Test Track and Mission Space). Then we entered Epcot on the left side of Spaceship earth near the bathrooms, headed around the left side of the World Showcase, finished up past Spaceship Earth again, then left the park near the kennel/stroller pick up area. It was a lot of fun for me and my son. My husband did the 1/2 marathon that year.
I was supposed to do the 5K again last year but got sick the night before, so my son and I didn't do it. Husband did the full marathon last year.
This year, the two of us are going the 5K, my husband will be doing the 1/2 marathon on Sat (and finishing before we start the 5K). Then on Sun my husband will try to complete the Goofy Challenge and do the full marathon.