This is the same for MLB and high school. Pustulio is correct. R1 gets home and BR gets 2nd.
7.05 Each runner including the batter-runner may, without liability to be put out, advance—
(g) Two bases when, with no spectators on the playing field, a thrown ball goes into the stands, or into a bench (whether or not the ball rebounds into the field), or over or under or through a field fence, or on a slanting part of the screen above the backstop, or remains in the meshes of a wire screen protecting spectators. The ball is dead. When such wild throw is the first play by an infielder, the umpire, in awarding such bases, shall be governed by the position of the runners at the time the ball was pitched; in all other cases the umpire shall be governed by the position of the runners at the time the wild throw was made;
Runners are always awarded two bases on an overthrow from a fielder (one from the pitcher). The question is two bases from where? It is from the time of the pitch when it is the first play by an infielder and it is from the time of the throw otherwise. Since this was the second play by an infielder, it is two bases from the time of the throw. R1 was on second, so he gets home and the BR was not yet to first, so he gets second.