It definitely affects transportation, since there are some significant road closures. For both the marathon and the half-marathon, the MK is the first part to be cleared of runners. The half basically runs from Epcot to the MK and back. Since the runners have to maintain a 16-minute mile, the MK should be cleared of runners by 8 or 8:30.
For the full, you run from Epcot to MK, then to AK, then to DHS, over to Boardwalk and then to Epcot. You might run into runners at AK, DHS or Epcot, depending on how early you get there and where you are. DW was a bit behind me in 2008, and she said that AK was very tight, since its pretty narrow anyway, and sharing the space between runners and park guests was difficult.
Now, for the Wine & Dine half - your guess is as good as mine. Until they announce the course (and the race start time), it's all just a guess.
The route the runners take is pretty well marked, and if you are visiting MK, or Future World at Epcot, you should have minimal interactions with the runners. If you want to hit AK or DHS, you will see more of them, but even so, by noon, they'll be about done.