The endgame occurs when you are no longer using middlegame methods such as large-scale rebuilds, but are instead focused on local wiggles, local pulls with very short rubber bands, and other methods designed to eke out small numbers of points on a basically completed structure.
Endgames often focus intensely on the lowest scoring sections of a protein, aiming to pop them into place in ways that do not greatly disturb an otherwise strong configuration. Thus, in the endgame, using relative score coloration is nearly essential, since the differences in local scores among different sections of the protein will tend to be tiny. You will also want to use the undo graph to monitor the score, because endgame changes are often minute, and because it is common to gain only fractions of a point at a time in the endgame.
My first in hopefully a long string of videos showing an endgame technique