Zero is set when you turn or or reset your arduino. Move it by hand to where you want 0,0,0 to be and its done, easy.
I need to put this in the FAQ’s but this is pretty much how it is done on a large cnc. An edge finder is used to set x and Y zero and the we always touched the top with the spindle on for the Z. That is how I do it now but don’t bother with an edge finder because Nothing has every needed to be that precision yet.