Basically the procedure would depend on the gcode program you have. If the gcode define the top surface of the workpiece as Z=0 then you'd touch off the workpiece surface and, zero your Z DRO, jog up to clear the workpiece (you don't want the spindle to start while the cutter touches the workpiece) and run the program.
If, on the other hand, the gcode defines your Z=0 at say the bottom of your vise, then you'd touch off the bottom of the vise, set the Z DRO to zero, jog up, clamp your workpiece and run the program.
Hope it answers your question.
Daniel