The way I calibrate my machine is use a digital caliper or digital dial caliper and execute a standard movement. For instance, with a 6" digital caliper, I’ll have the machine jog 6" and then clamp a caliper to the spindle gantry somewhere and have it against a fixed position on the wasteboard. Just make sure you the caliper or dial indicator parallel to the axis for the highest accuracy. Then use the numbers to calibrate. With a dial caliper I’m usually moving the spindle around 1", but with a greater degree of accuracy over the shorter distance. If I’m machining something where deflection and material hardness might affect my numbers, I’ll use a 1" calibration pocket and adjust my machine to that.
based on what you’re saying, I think you mean calibrating the Z-axis, as that would directly effect the depth of cut. Either way, both will work.
if you come in light on an engraving and you want more depth, keep the same X/Y zero, and select manual instead of probe for your Z axis, and bury the bit however much deeper you want the cut.