I know a lot of people on here can give you all sorts of good ideas for watching the marathon, but here's the first question: where are you staying? This will make a big difference for your strategy that morning. If you are on site, you have the option of taking the buses (rented tour buses, not official Disney buses) from the front of your resort to the starting line at Epcot, and from there you can take the monorail to various viewing points along the course.
I know last year as we were preparing for the marathon and our viewing locations, everyone said that the monorail was the best method of transportation that morning. I didn't fully understand this until I was there on Saturday morning for the viewing of the half marathon. The monorail is running very early (approx 3am), and it can transport you from the starting area at Epcot to the TTC and Magic Kingdom, which are both great viewing spots for the marathon.
Here's a brief rundown of what we did, and it seemed to work well. We had spectators on both Saturday and Sunday, and each of the groups followed this same plan. We--the spectators--drove from our resort (POFQ) to the Epcot parking lot around 5am. I would really recommend that the marathon runners in your group take the specified Disney buses to the starting area. The whole process is run pretty efficiently. Anyway, the spectators drove to Epcot and parked in the main parking lot. We then hopped on the monorail and headed for the TTC. It's up to you, but I would not recommend trying to watch the start of the race. No way are you going to be able to spot your runner at mile 1 of the course as thousands of runners go by. The viewing area at the start is not that large, and I saw people stacked three and four deep along the side. If you skip viewing at the start, you'll give yourself more time to get a prime spot later along the course. Once we got to the TTC, we found spots along the course right across from the Disney kennel (near the tunnel where the runners go under the main road in front of the TTC/Polynesian). We had already talked amongst our group, so that the runners knew where to watch for the spectators, and vice versa. I know on Sunday when I ran through this area, I was prepared to find my family as I knew exactly where they would be standing. It's easier to find your runner if you are both looking for each other in a designated spot.
After we saw the group at the TTC, we walked across the Polynesian parking lot to an area along Floridian Way (this was approx a half mile walk) where the runners pass after they have gone through the MK and along the Grand Floridian/Shades of Green. There is about 3.5 miles of marathon course between the TTC and this location, so you shouldn't have too much trouble "beating" your runner to the viewing location. If you were to try to watch from the TTC and also watch in the MK, I'm not sure if you would have enough time to get there as you would need to reboard the monorail and get through the gates of the MK and onto Main Street before your runner got to the same location. You would probably need to pick either viewing at the TTC OR the MK, not both.
After seeing them on Flordian way, we made our way back to the TTC and took the monorail back to Epcot. We were then able to watch the runners from the grandstands near the finish as they came into the finish area. Tip" don't watch from the grandstands right at the finish line for two reasons. 1.) The finish area is VERY crowded and there is little chance that your runner would actually see you 2.) The runners are so excited at this point, they probably will not be looking for you in the stands. We chose to view from the very first grandstands which are approx 0.1 mile from the finish line. Just keep walking all the way to the right as you approach the grandstands, and when you can't walk any further (because you'd end up backstage), you're there.
This strategy worked very well for the half marathon as it gave the spectators enough time to see the runners at three locations along the course and also enough time to travel between viewing locations. Using this strategy for the marathon works as well, but keep in mind that you won't see your runner from mile 12 until mile 26. This is a long stretch. I'm going to be running the full marathon again this year, but if I was viewing it, I may try to hop a bus to the AK to see the runners at mile 17 as well. The only problem with this is that there is only one road into and out of the AK area, and this area can get congested as the morning goes on. My only concern would be getting stuck in traffic and not being able to see the runners at the finish line.
Ok, I've typed way too much, but you got me excited talking about the marathon weekend. Like I said, I'm sure everyone can give you all sorts of strategies and what worked well for them, but hopefully this will give you at least one plan that seemed to be good for us. One last note--make sure you know your runner's anticipated pace throughout the race. Knowing this will allow you to figure out when to look for them at certain places along the course.
Hope this helps.
Steve