Basically you just load WinBoard with the engine you want and then click MODE and then EDIT POSITION. Then you can right-click and bring up a submenu to drop particular pieces on squares, clear the entire board, etc.
Once you have the position you want, with the color to move that you want, you should be good to go. I'm not sure why your engines are exiting unexpectedly. Are they ALL doing that?
Chess Engine

Does anyone know how to set up a position in winboard that a chess engine like chess kiss or mustang would play out with me? When doing so, the engine just exits unexpectedly. It needn't be these two engines but I wanted to play my opening positions against weaker chess engines to practice with some chance of winning. I already know how to do this with fritz but on weaker modes it just makes random blunders that I doubt a real 2200 would make. Thanks so much!