Normally you right-click where you want to place the separator.

Have you been having any other problem with bookmarks/history?

Places Maintenance {web link} Allows to run Maintenance tasks on the database that drives Places, the bookmarks and history module behind Firefox.

Open the Add-ons Manager. Locate the add-on and press the Options button. Then follow the directions.

Note that in the Bookmarks Manager (Library) you can only add a separator in the right pane (in the left pane it is grayed). You can also add a separator in the "Show your bookmarks" and Bookmarks menu drop-down list via the right-click context menu.