If you hit Stop when the axis was in motion you need to re-home your machine as there is a chance it has lost position. Under normal circumstances you should press Hold first and after motion has stopped then you can safely press the Stop without losing position.
To do a Run from Here you can scroll through the code and watch the toolpath display to see where you are, once you get to the position you wish then press the Run from Here button. As Daniel said you need to check that the prep move is correct before you restart,
If however you have the demo version of Mach then Run from Here will not work.
Hood