I applied to both kinds and ended up with one acceptance each (1 MD and 1 DO). None of the schools had a problem with it, and it came up at several interviews. When I interviewed at MD schools and told them, they just said it is all the same anyway. Same deal when I interviewed DO and told them I had interviewed at MD schools. It really IS the same thing, and doctors on both sides know. You really don't need to explain yourself for applying to both kinds.