Makerbot operator can also yank the belt to raise or lower the z-axis manually. This is done:
1. At the beginning, when you are centering the build platform and putting the nozzle right a 0,0,0
2. During the raft printing, to squish down the plastic.
3. At the end, if you haven't programmed in a lift at the end of the build.
To make sure I never made a mistake, I drew an arrow on the cabinet showing which way I should yank to raise the printing head!