In the perfect world....runner advancing to 3rd is out....but, as you wrote...he was most likely going to be safe...so I would score it as a single, with the runner advancing to third by the batter and then the runner advancing to second on the throw.... Then I would score the runner advancing home ...

So...I'm going to relate it to little league baseball, as that is how I use the app... Generally speaking....when you hit play, and the lineups show up for both teams...You should select the starting player for each position, including the pitcher. Then you click done. When you click play! in the bo...

I would imagine that you initially scored the batter with a homerun...which automatically scored the runner from first...
I would hit undo and then click on the runner on first base, click that he is out, click on third base, click missed Base, then score the homerun from the batter.