Seems like the application menu plugin have a nice shortcut for the settings manager for quick access. But whisker menu plugin and appfinder does not. In both whisker menu plugin and appfinder i can not see settings manager unless i select "all" and scroll the long list (not so easy) or i type (have to use keyboard). Would at not been smart to have settings manager as the first item in the settings menu in all three applications (application menu plugin, whisker menu plugin and appfinder)? Just like "run program..." and "application finder" is first in Accessories category (application menu plugin, whisker menu plugin have this but appfinder does not seem to put them first). That way it will be easier for the users to find and open system settings. A place they might have to visit a lot. And have it consistent in the three applications.
Whisker Menu doesn't control the order of items in the menu, it just uses whatever garcon says the order is (or sorted alphabetically, if that is what the user has picked). This would need to be configured in the default Xfce menu items, and then Whisker Menu would pick it up automatically. Additionally, the settings manager is available by default as one of the command buttons in Whisker Menu (next to locking the screen or logging out).