I usually keep two Glacern 6" vises on my Tormach 1100. These were purchases as a matched set so the heights at key points are better than 0.0005". I have a Saunders fixture plate on the mill and tram the vises so the fixed jaws are at the same Y. Both vises are loose shot to the table, then set an 18" gauge block in the vises (movable jaw has a 1" Delrin round so the jaws don't cover the 1/2" attaching screws). Tighten the LH vise LH cap screw and run an indicator onto the gauge block face at that X. Then move the table so the indicator is on the gauge block at the RH cap screw of the RH vise. Tap the vise as needed to match the indicator number from the LH side. Then run back to the LH vise, LH cap screw to verify. When things look good, tighten the other two cap screws.
I've never run a CNC job on one vise while removing work from the other, though it'd be possible. My use has been for holding long stock; makes the vise into essentially a 12"+ wide vise.
Bruce