On overthrows that go out of play, the maxim “two bases from the field, and one from the mound” is used to describes how many bases the runners receive as an award. Usually the trickiest part is whether you give the runner their bases from where they were at the time of pitch or at the time the throw was released.
There is one more tricky thing that can happen. It is possible that a runner will not get the full two bases he deserves.
The situation is even hard coded right into the rule book.
Rule 7.05(g) Comment: In certain circumstances it is impossible to award a runner two bases. Example: Runner on first. Batter hits fly to short right. Runner holds up between first and second and batter comes around first and pulls up behind him. Ball falls safely. Outfielder, in throwing to first, throws ball into stand.
APPROVED RULING: Since no runner, when the ball is dead, may advance beyond the base to which he is entitled, the runner originally on first base goes to third base and the batter is held at second base.
In this play the options are give one runner 3 bases or give one runner 1 base. The rules say to give the trail runner only one base. What is not said in the ruling but is somewhat obvious – one base and two runners is a no-no and this would happen if both were awarded 2 bases and 3rd base.
When placing runners the umpire will always start with the lead runner and work backwards.
Some people read this situation and mistakenly try to apply it when there are two runners between 2nd and 3rd with a ball thrown out of play. In this situation both runners are allowed to score. Why? Because this is not a situation where two runners would wind up on the same base. They would both be on no base, in the dugout drinking water and slapping fives.
Awards on balls thrown out of play is on page 60 of RuleGraphics.