My dad was a shop teacher and taught the 2-chuck key method. He'd marked the face of the chuck next to the jaws with "A1, B1, A2, B2" going around the chuck. Set the stock in the chuck and ran the jaws to loose contact. Used a dial indicator on a mag base (no QCTP's in those days) and swept A1 to A2. Zero'd on A1 and flipped to the opposite side so A2 was at the indicator. Then adjusted both jaws to take A2 half-way to zero. Reset to Zero on A2 and rotated back to A1 for confirmation. He'd get within a couple thousandths pretty quickly, then did B1/B2. For the final adjustment, he'd just tighten one jaw to hit zero.
For square stock, he'd use a couple of methods. One was basically the same as that above, but he had the kid roll the chuck back/forth slightly to find the low point at the indicator. Zero out, pull back on the indicator so it's off the work and rotate the chuck 180. Do the slight roll back/forth to the low point and leave the chuck there. Then do the two chuck key adjustment to half-way to zero.
Other method was to have the student use a square or surface plate and height gauge to scribe the center point of the square stock. Then center punch it by eye. Mount it in the chuck and put a wiggler with a sharp point in the tail stock, engage the wiggler end into the center punched hole. Then use the procedure at the top with the wiggler in the center punched hole, indicator on the wiggler probe shaft to find center. He used this same method for oddball stuff like an eccentric hole.
Once you do it a few times it goes pretty quickly. You'll easily get dialed in within 0.0005" within a few minutes with practice.
Bruce