The marathon course has some changes for 2020 and the specific map [or changes] hasn't been published yet. I know that some of the key spots will remain the same so can tell you that using Disney transportation or Minnie Van from Poly is a good idea. Even with the road closure the buses are still pretty efficient. To answer your specific question, the marathon starts at 5:00 AM with various stages/staggering of runners so the last group will most likely go off around 5:40ish. Pre-race activities get going around 3:00. First stage of the marathon runs from Epcot to MK, then MK to AK, AK to BB, BB to HS and then through the Epcot resort area and into Epcot. With a 16 minute/mile pacing requirement the course should be completely cleared by 12:45 - 1:00 PM. MK will clear first, AK second, then HS [proabably noonish] with Epcot and the Epcot Resort areas last. This is why the Friendship boats are suspended until around 1:00 PM.
Having said that, no one knows what exactly the course changes are yet so my assessment might be wrong, but I'm pretty confident it will still hold to some degree. My advice to you would be to check the RunDisney site for race specifics closer to the actual marathon weekend. It's hard to say when they will officially drop the course map and event guide. Also, your resort will have published information on race weekend impacts and CMs will also be able to answer specific questions! You will get to HS!