TD Prefs 2 doesn't directly replace ToolsPrefs yet as ToolsPrefs has 1 redeeming feature. When you save your Menu Toolsdaemon is automatically updated.
Until I work out how to do this you can use ToolsPrefs to Update Toolsdaemon by saving your Menu from TD Prefs 2 then load ToolsPrefs (From the Menu Tools/ToolsPrefs) and Hit Save again.
The other alternative is to after saving your menu with TD Prefs 2 quit Toolsdaemon and reload it.