To start, all the axis are sent home by a home command. Each axis eventually hits a switch when the axis is at home and the software sets the axis to zero (or some other number as chosen by the operator).
I home my machine, the axis get set to x=0, y=12, z=3 (cutter to the far left, back, and up). This allows for easiest access to the table for placement/clamping of stock.
The machine just goes from there.
Another option is to forget home switches and just move (jog) the machine to the corner of the stock and manually set the axis' to zero.