we were in the middle of all the action last year. you just can't avoid it.they run through the parks which is kind of neat to see. you'll find yourself "cheering" them on. there are LOTS of people and the parks are VERY crowded.
Just avoid the park they're running through (Epcot) and you'll be fine. We were that last year too during the marathon and we had zero problems. Any slight increase in the crowds was over a day after the marathon.
FYI the half marathon (Saturday) only runs through Magic Kingdom before it opens and then through Epcot (front part)
The full marathon (Sunday) runs through Magic Kingdom (before it opens), Animal Kingdom, MGM AND Epcot.
Both races finish at Epcot.
If you're driving yourself what will probably affect you the most are road/lane closures in the early morning. (Both races start at 6 a.m.)
Last year I ran the half (this year I'm doing the full). When we went to AK Sunday morning it was a bit harder to get around as the sidewalks were partly closed for runners.
Please do cheer on the runners; it is very helpful and more appreciated than you'd guess. Also, if you are in a park PLEASE be careful about trying to cross in front of runners. We're tired and our reaction times are slow!