There are a lot of “standard” ways to do the coordinates, but the one that makes the most sense to me (and Ryan’s tutorials follow this logic, probably because I learned here) is to have Z=0 be the top of your workpiece (the thing you’re cutting) and have it cut deep enough to cut through.
The work starts in the CAM. I hope you’re using the EstlCAM basics tutorial to get that all configured. EstlCAM needs to be configured so that when it’s not cutting it’s up above the work (at Z=5 or something) and when it is cutting, the depth that it is cutting is in the negative. So if you are cutting at a depth of 6mm, it will be at Z=-6.
The other part is X and Y. You can have the origin (X=0, Y=0) at the lower left corner of the design, or right in the center. Putting it in the lower left is easy amd great for saving material. Putting it in the center is great if you’re carving something on an existing thing and you wamt it centered (I carved a design into a cabinet door once). You need to choose the origin in the CAM and then set up the machine with that origin.
Once you have the CAM doing that (and if you’re using the crown gcode, then that’s done), how do you set up your job? You move the tool to the X,Y origin and move the Z until it’s at the top of the workpiece (not the top of the spoil board). Then your reset that to 0,0,0. Then you move the router up a smidge, start the router and then start the job.
Also, the entire surface won’t be flat. Even if you think it is. So if youre cutting through 6mm ply, don’t set your cut depth to 6mm. Add some slop. That’s why you have a spoil board. If you’re cutting a coaster, it will be pretty flat in that small area, so 0.5mm is enough. If you’re cutting a stool, you might need 2mm and if you’re cutting a dresser, you better know what you’re doing .
Talking about the coaster again. If you want the Z to be accurate, you need to set it where the coaster will be cut. If you set the Z to the right height and then move 1000mm in XY to start cutting, the Z will be off. I messed this up today on my printer carving. I set the Z height 16" or so away from the carving and it cut 3mm too deep.