Right-clicking on a note's icon in outline views opens a pop-up menu for selecting a prototype for the note (setting the note's $Prototype). Such a menu is only displayed if there are prototypes defined in the TBX.
If multiple notes are selected, using this method on any one item will update the prototype assignment of the whole selection (including any separators.
Although separators have no visible note icon, right-clicking a selected separator at the left-most end, where the icon would otherwise be, will show the prototype pop-up menu.
Setting a prototype on an alias sets the original note's Prototype value.
This method also works in Chart, Attribute Browser and Timeline views.
This is just one method for setting a note's prototype.