Ok machine coords are normally when the tool is lower left corner and fully up in Z, that will represent X,Y and Z zero. Because your home switches are not in these locations you need to set up Home Off values in Homing and Limits page. The values you set are the distance that each axis is away from the machine coords zero. When you home the machine coords will then be set to that home off value.
Pressing the zero at the side of the X, Y Z DROs doesnt alter the machine coords, it sets a work offset zero position so that you can zero at any point which is convenient for the work in hand, the machine coords stay unchanged and thus Mach still knows where it is in relation to your axis travels..
Hood