Jim,
You are correct in how a ship is put on keel blocks, I did that with the USS Honolulu (SSN 718) in '93 and yes the drydock was set up for a first flight 688 keel block layout (i.e. the blocks are different heights to match the keel curvature) once the boat is over top of the keel blocks and verified by divers the drydock is then slowly drained (it takes hours to complete) using numerous divers verifying its position constantly until it is firmly setting on the blocks.