all the info you need is in this forum and cnczone to do with those machines look and read all your answer are there.

you can set your soft limits set for z, x, y depending where you set your work start point i.e. left front corner so set x,y soft limits negative to -1, positive to end of travel for x and y. for your z just have a spot at the top of your z axis where you can ref it, move it down to top of work pieces zero it, as long as you turn soft limits of before you do this then turn them back on when everything is set there is less chance of crashing the machine as m3 will let you know there is a problem. and set your safe Z to 5mm.

I don't even use any limits at all on my big machine I just ref all home at a safe spot then zero it at work zero.

just remember m3 is a dum system it need to be told what to do, where its home is where its work is at