An annotation is the value of a keyword contained in a FCS data file. I guess the best-known keyword is "Sample ID". Annotations can only be added to plots. When the data file of the plot changes, the annotation changes accordingly.
To add an annotation to selected plots, use "Annotation" of the "Plot" menu. A dialog will allow you to select the wanted keyword. If multiple plots are selected, the annotations will be added to each plot but the dialog will display only the keywords of the first selected plot. A plot can have multiple different annotations.
If a plot has multiple overlays, the annotation keyword for each overlay is shown. The "Legend" is a color label based on the respective overlay's color scheme, and can help to link the annotation with the respective overlay.