Mike, here is a little info I copied from another thread to help you some I hope.
Stick your left hand in front of you, point your thumb up, first finger ahead and second to the right. That is the +ve direction of the three axis (Thumb is z, first is y and second is X). Also remember that it is the tool direction and not the workpiece/table. so on a mill, quill going up is Z+ve, table towards you is Y+ve and table to left is x +ve.
Not sure about the figures, haven't looked.
Reversed changes the direction the motors will go in for a command. If you tell your x to - and it moves +, you can fix that here.
That makes sense to me. Z home is usually as far away from the work as possible. Any time it gets closer it is going - and a - number is less than 0.
Negative IMO, but you can set it up to suit you.
It should be on at all times if that's what you want. If it is all set up right, you can leave softlimits on all the time and when referencing the axis Mach will know it can override that to ref.
Brett