After finishing a bowl I mark the center of the bottom while it is still on the chuck (I use an inside gripping chuck). I found a length of metal tubing that is the same diameter as the through hole of the headstock and installed a pencil inside the tubing (using masking tape to make it fit). I stick this through the headstock until the pencil point touches the underside of the bowl, then turn the bowl 1 turn by hand, while holding the tubing. If the pencil is centered it makes a dot, if not it will be a circle. To mount the bowl on the vacuum chuck for finishing the bottom, I bring up the tailstock and hold the bowl against the vacuum chuck with it, the point of the live center in the dot. As I turn on the pump I crank in the tailstock so that it remains in contact with the bowl until the desired vacuum is reached. This achieves a near perfect centering the first time.
Clear as mud?