When Prism performs simple linear regression, it automatically superimposes the line on the graph.
If you need to create additional graphs, or change which line is plotted on which graph, keep in mind that the line generated by linear regression is seen by Prism as a data set. You can add lines to a graph or remove lines from a graph on the 'Data sets on graph' tab of the Format Graph dialog.
If you check an option on the simple linear regression dialog, Prism will create a results table with residuals, which are the vertical distances of each point from the regression line. The X values in the residual table are identical to the X values you entered. The Y values are the residuals. A residual with a positive value means that the point is above the line; a residual with a negative value means the point is below the line.
When Prism creates the table of residuals, it also automatically makes a new graph containing the residuals and nothing else. You can treat the residuals table like any other table, and do additional analyses or make additional graphs.
If the assumptions of simple linear regression have been met, the residuals will be randomly scattered above and below the line at Y=0. The scatter should not vary with X. You also should not see large clusters of adjacent points that are all above or all below the Y=0 line.
See an example of residuals from nonlinear regression.